There are a number of issues that you mention in your question. I think for some of these there are things that you need to look at yourself rather than blame the manager.

Let's address them one at a time:

...it's reached a point where I'm no longer willing to keep inconveniencing myself if there isn't an answer to 'What is the actual benefit to the team or problem being solved by this change?' that I feel is acceptable.

As in my comment, is this something you have actually asked your manager? Have you outlined any negative impacts that the change will have on your team, such as ramp up time, decreased productivity, no measureable increased productivity. If you want to counter this argument, then you need to give evidence as to why it's a bad thing.

My thought process was along the lines of 'What are the repercussions you can leverage against me if I say no? You can fire me and I can have a new job within days,' but I felt that communicating this wasn't appropriate and would lead to an unhealthy work environment.

Yes, communicating this is not appropriate and speaks more about you than your manager. If you have a moral objection to something that you cannot back up with a rational argument, then it's your problem that you need to deal with. If this means moving on and finding the same situation (yet) again, then hopefully by that time you may find that the issue resides with you rather than the organisation.

I usually bring a book with me and split my attention between reading and paying attention to the meeting. I was pulled aside and told that I need to stop bringing books.

This is incredibly rude and unprofessional. Your manager has for whatever reason decided that he or she requires your input in this meeting. You objected and were told that you need to attend. If I had someone doing this in my team, they would be pulled up on it immediately. Just because you don't see the value does not give you grounds to act in an unprofessional manner.

This question may be specific to high-demand professions (in this case, software engineering), but is there any diplomatic way to explain to a manager that they should be picking and choosing their battles?

I think you should rather be asking yourself if you should pick and choose your battles. From how I read the situation, your manager has not done one thing wrong; instead I see a rude, disruptive and arrogant team member who does not wish to act in a professional and objective manner.

Is picking up your bags and leaving the only solution?

This won't solve anything, because the issue will travel with you to your new employer, like it did to where you are now from your previous workplace.

What I would recommend is this:

If you have an issue with something you are being asked to do, quantify the reason for it. If there isn't a reason you can give legitimately, then nobody is going to say no.

If you have been asked to attend a meeting, try engaging with the managers rather than sit there passively. Be proactive. Perhaps you might find out earlier some of these decisions you are having "thrust upon you" and have a chance to provide input sooner.

I'm sorry if this sounds harsh (and I may well get downvoted for this answer), but as someone who has been a developer for 20 years and have sat at all levels in the reporting hierarchy, it's important to recognise where you should perhaps be introspective and look at how you can improve yourself and the work flows, rather than acting in an unprofessional manner that does you no favours.

Too many times I have seen someone who is bright, very capable, and instead of trying to resolve an issue, they simply complain about it and contribute to it instead by not being proactive and giving guidance from their experience that could make things better for everyone. This is what I see in this post.