I think they are basically an attempt at form of "issues/tracker bankruptcy" -- we have too many open things here, leaving them all open like we're going to get to them all eventually is a fantasy, and is overwhelming and makes it harder to find the ones we might actually address, so trying to algorithmically close the ones least likely to be actionable is just trying to make the situation more manageable.
I think it's a desperate measure -- if any maintainers are seeing it as reasonable management technique rather than desparate measure, I think they're making a mistake. It has a lot of downsides, some of which you outline, I agree with you. It also generally raises user frustration, leading to even more adversorial relationship between users and maintainers, which is what the OP is about and I think part of what's going on in this "issue bankruptcy" situations too.
Notably, Rails just turned off their auto-closer for Pull Requests (not sure about Issues), with this commit message from a maintainer:
> While the idea of cleaning up the the PRs list by nudging reviewers
with the stale message and closing PRs that didn't got a review in time
cloud work for the maintainers, in practice it discourages contributors
to submit contributions.
> Keeping PRs open and not providing feedback also doesn't help with
contributors motivation, so while I'm disabling this feature of the bot
we still need to come up with a process that will help us to keep
the number of PRs in check, but celebrate the work contributors already
did instead of ignoring it, or dismissing in the form of a "stale"
alerts, and automatically closing PRs.
https://github.com/rails/rails/commit/acf48169943011834c4c88...