It always bugs me that I have to re-run my previous WP-CLI command when it detected & installed an auto-update.

That's because of this line in Runner::auto_check_update():

I'm wondering: can't we just spin up the new Phar with the originally passed arguments in a subprocess?

This way, the user would get the benefit of the new features without the hassle of having to manually re-run the previous command.

Alternatively or additonally: pass --yes to cli update by default to disable the confirmation prompt (of course this should be configurable with an env var).