@MastodonEngineering I haven't seen any major problems with the rbenv method since like early Mastodon 3.x days.
Release-upgrades of the underlying OS (Debian here) can be somewhat fiddly, but the last time around, running a bundle install --redownload in our ~/live directory after the OS upgrade rebuilt everything correctly.
I think the Ruby updates accumulate some cruft over time since old versions are not deleted?