(Side note: just so others can get a sense of where opinion on this post lies, that +3 you see at the left as of this writing is the sum of 28 upvotes and 25 downvotes. The following seems to be a divisive opinion.)

I don't think one can give a "neutral summing up of the issues" because the one core issue here is so non-neutral and divisive, despite being hidden to some degree (and hidden purposefully by those arguing one side of it).

The elephant in the room, as I now see it, is that a substantial number of people on SE dismiss the concerns of certain non-mainstream people and how they're made to feel unwelcome in ways not obvious to those dismissing these concerns.¹

SE has not dealt with this in the best possible way, and has even made some serious mistakes, but that doesn't change that they were doing something to address a problem for these non-mainstream people. Unfortunately, those who want to dismiss the concern SE was trying to address have leapt on these mistakes as an excuse to promote their agenda of, "we mustn't address or even think about the problems of and non-welcoming attitude toward those non-mainstream people."

Below I will discuss one reply that exemplifies this core problem, a problem that I've seen recently in a large number interactions in SE on this topic. After the example I'll give my personal views on what I see as the main issue.

In one of my recent comments² I said:

This protects Christians just as much as anybody else. If I say my religion requires that I call you "she"/"her" etc. you might quite rightly be annoyed if you prefer "him" and I refuse to use that. If you take your argument to its logical conclusion, you can do nothing about that because insisting on being called "him" would be "forcing me to tolerate" that. I instead say that you get to pick whether you want to be "him" or "her"; and I just extend this to everybody, rather than limiting it to the people who pick what lines up with Christians' choice.

The reply contained a number of points, all of which are bad or irrelevant arguments being used as excuses for denying the validity of the problem.

I've never seen one get mad about that kind of thing online, in regards to some random poster on a forum.

In other words, "I don't see it as a problem, so we need not address it." The idea that certain minority problems are not problems that need to be addressed is the basic problem here.

I have, on the other hand, had a transwoman attack me with a bunch of angry PM's on the Kerbal Space Program forums when I referred to them as "he", because I didn't read their profile.

That things happen on other forums that would not be condoned on SE under the old or new CoCs is so staggeringly irrelevant to rules for politeness on SE that I can see it only as an attempt to mislead, particularly when it identifies a member of a minority group (and makes that their primary identifying characteristic) and then goes on to say, "they attacked me."

If this is not a deliberate attempt to put a minority group in a bad light, that's all the worse. Not being conscious that you have a "those annoying minorities are causing me problems" attitude makes the problem even harder to address.

Online, especially on sites like SE, your gender isn't relevant to the conversation.

Again, complete dismissal.

When someone starts calling you by the wrong pronoun it may not be relevant to the topic, but it certainly is relevant to the communication. Nobody would argue that there's not a problem if I start or continue referring to a mainstream male "George" as "she" after I've been asked by him not to do that. Yet if it's a person where a substantial number of people, for whatever reason, don't agree with the pronoun or gender that person has chosen for him/her/whateverself, people start finding excuses to try to erase the problem, as above.

I am male. I wouldn't get mad if you called me "she", in the course of a larger discussion, because which gender pronoun you use almost certainly has no bearing on whatever we're talking about.

Again, "it's not a problem for me and maybe not even other people I personally know, so I've decided that your feelings don't count and you must accept my decision that it's not a problem for you, either."

Replying "I don't have this problem" when someone else states a problem they have is nothing but dismissive.

We're not talking about consistent harassment in PM's, which is certainly against the old CoC...

So, the poster introduces exactly this topic in a way that puts a minority group in a bad light and then says, "don't discuss what I just did there."

...we're talking about someone using whatever pronoun they happen to pick for a random user they know nothing about.

Except we're not. We're talking about people who, after they've been informed of someone's preferred pronoun, insist they have a right to refuse to use it. The "I didn't know the correct pronoun" argument has been addressed time and time again in the last week or more, and we should all be able to agree that if you didn't know, you get gently corrected and everybody moves on. But no, people have to keep bringing up this straw man, which only inflames the argument. This is not arguing in good faith; this is an attempt to derail the real argument and preserve the status quo.

Why should that person be forced to pay attention to something as meaningless as getting the right pronoun? At best, it's just an unnecessary nuisance, worse it could impact the readability of their post.

And what a great summary: "I refuse to see your problem, I've just erased it, and you'll have to accept that. My concerns are far more important."

This whole brouhaha has been pretty enlightening for me. Lack of acceptance of non-traditional genders turns out to be very widespread in SE, or at the very least there's a not insubstantial and very vocal part of the community willing to defend lack of acceptance.

It seems that over my past decade here I too have suffered from a classic case of, "it wasn't my problem so I didn't see it." (And I probably suffer from that to some degree still.) I probably also am to some degree part of that problem; I imagine there will be times when someone's preferred pronoun feels weird to me to use.

But these are all reasons why I must step up and say, "Yes, when someone asks me to use their preferred pronoun, I will do so, and I will not question it." I, without even thinking consciously about it, expect that myself, and pretty much automatically I get that myself (which is why I don't think about it). I need to consider others who don't happen to be in that situation.

This is not to say that there aren't other issues that need to be dealt with, other ways in which SE management has gone wrong, or even that this particular issue could not have been dealt with better. But it's incumbent on the people bringing up those side issues to make it clear that they agree that everybody has the right on SE to be addressed by their preferred pronoun before they start diving into (or, less charitably, bikeshedding about) the details of how that's done because there are clearly people here who do not agree with that at all and who are using the details as cover for their disagreement with that core issue.

As for those who really don't agree, it's unfortunate for both them and those of us who remain that we lose their valuable (I do not use that term sarcastically) input on other topics. But sad as it is, I think it's better to take a hit on this than to throw some non-mainstream people under a bus yet once again.

¹ In some cases this denial is based on outright denial of facts, through either ignorance or malice, and via explicit or implicit claims. As we can see from a comment below, some people claim that gender is no more than sex. While the gender vs. sex terminology distinction did not exist in western societies until 1955, it existed even back to ancient times earlier in other societies, such as with the Hijra in India. Further, even where there was no language for the distinction, the distinction still existed: a skirt or dress has long been considered feminine clothing in later western society (except when it isn't) despite the standard men's wear in ancient western society being a garment that we would now call a dress; these are clear examples of a societal, not biological, standard. Beyond that, biological sex itself is clearly non-binary, both overtly where the individual shows both male and female external genitalia and more subtly where chromosome 46 does not match the common external genitalia associated with it.