I do not understand why a question about issues with archive.is was migrated and now put on hold, whereas questions about archive.org date back to 2010 (probably before Web Apps SE was even created, due to incoming migrations), which is tagged on 24 questions.

How's archive.is so fundamentally different from archive.org as a webapp as to require such actions?

Are moderators trying to advance an agenda against popular independent sites without venture capital? Where's the explanation for the reasoning of a misplaced migration of the question?

The archive.today website is certainly a webapp. Questions about quirks, bugs and peculiarities in gmail, facebook, youtube, twitter, google-search, github, dropbox, reddit, and many other websites, are all on-topic here (per my understanding — please correct me if I'm wrong), so, it's unclear what makes you judge archive.today any differently, and why its unavailability with Cloudflare dns (25 Qs) is somehow offtopic. In fact, as mentioned above, we even already have archive.org tag with 24 questions, as early as early as 2010 (due to incoming migrations). How's archive.is any different?!

Looking at https://webapps.stackexchange.com/tags, many of these most popular tags don't even qualify as a pure "webapp", either, if that's the rationale for exclusion — e.g., google-search is never really referred to as a webapp, yet it's all deemed on-topic with 686 questions, and is a top-13 tag.

Likewise, it can also be argued that 1.1.1.1 itself is a webapp as well (this is where we get a bit of an intersection with some other sites on SE network), however, this question is very specific about archive.today, and doesn't go into the whole performance and other unrelated issues around 1.1.1.1 (Hacker News discussion revealed that there are many more than were mentioned), so, it's definitely on the WebApps side.

If anyone disagrees with the question or the answer, they're free to downvote. The number of upvotes greatly exceeds the number of downvotes on both the question and the original atomic answer that came with the question; this is the case even with the alternative answers available, which haven't gotten quite as many upvotes even after being posted around the same time, and I think this proves that the original question and answer pair are neutral enough.

The question received 39k views in less than 48 hours, 63 upvotes, and only 2 votes to close.

Why does the moderator feel a need to intervene with such a popular question that's welcomed by the community?

Clearly if it was actually offtopic, the community would be capable of attaining the 5 close votes that are necessary in order to close the question by itself, and/or downvoting into negative territory, especially given the amount of attention it has received — alas, that's not the case, vast majority of the votes are upvotes, yet the moderator feels a need to censor for no explained reason.