Sorry for the trouble here! Honestly, I think the odds of Versions going away are low-to-nil, but that doesn't mean that we can't try to make this work better for you.
From my work in various apps that support Versions (not just our own), it looks to me like "on reopen, put the document back exactly like I left it" is intended as a feature.
Sounds like you'd prefer it if the app handled content changes differently from view-state changes, at the very least. I'm not an engineer, so I can't really speak to what's possible here. If you email that and any other suggestions you may have on making the Versions support work better for you to the
support ninjas, we can make sure the rest of the team sees 'em. Thanks!