Oh - I haven't come across any issues like that and I believe its used as the parent for a few themes (Elegance for example) as well as my Flexibase - although that actually uses flexbox to replace the bootstrap grids, so wouldn't have the same issues. I'm sure if you report any issues Bas would look at them - he is very active at maintaining this theme and ensuring it keeps track with the latest versions.
No, the new theme_boost is a completely new theme built on BS4 while bootstrapbase will continue as it is as the parent for clean, more and the series of themes that people have built on BS2 - no major changes to those in that respect! Boost will sit alongside bootstrapbase, clean and more for a few versions. Then if history repeats itself, clean and more will move to the plugins database, while bootstrapbase remains in place for another few versions, before that too is moved out. But please don't ask me to define 'few' - I have no idea and am only basing these assumptions on what has happened with the non-bootstrap themes
As for naming, well after some of the 'fun' I had initially with theme_bootstrap, I would keep the name of any upstream library such as 'bootstrap' out of the theme name altogether, as they have with boost
And, in fairness to HQ, there's no major surprises for theme developers - bootstrapbase will continue as it is with BS2 (they are only just now planning the removal of base having moved the older non-bootstrap themes out of core into the plugins database several versions ago); bootstrap3 was never officially supported by HQ, the theme_bootstrap is a third party development by Bas; boost is a new development and will be based on BS4. There is certainly no history of sudden jumps leaving previously developed themes unsupported, or of dropping theme support without plenty of warning (as in multiple versions).
Richard