SUMMARY The goal is to prevent accidental merging of paint layer with vector layer. In case both paint and vector layers are selected, let there be a confirmation dialog before proceeding. That's all. I've made too many bad accidents because of that. Also, if you can, study Clip Studio's Frame manager for comics. The app has an auto gutter and paneling tool. With flexibility taken into account as it's always possible to edit/delete a panel, add/remove/displace/edit a gutter and whatnot. Such a tool needs to come to Krita. By God's grace it will. Amen.
Your second paragraph is an elaborate feature request and needs to follow the guide: https://docs.krita.org/en/untranslatable_pages/new_features.html - and it cannot be just added to a bug report, it needs to start on krita-artists.org to get feedback and ideas from artists, then get an official Phabricator task, it needs a mockup and a lot of other things. If you don't follow that route, it's unlikely anyone will start working on it. Copying some other program's features blindly is hardly ever a good idea: we don't want to be a copy of CSP or PS, we want to be *better* than them. For that, instead of blindly copying features, we have a process for features to get the best out of them, and you need to follow this process, otherwise it won't be implemented. Please do not ever make bug reports with more than one wish at once, and don't use bug reports for wishes like the one from the second paragraph. For the first paragraph: this is also unlikely to get enough support to be implemented, because confirmation dialogs are really disturbing in the process. And I know like adding an option to turn it on or off sounds like a good idea but in reality it makes the code of the program more complex, which makes it more bug-prone, which we'd like to avoid. Merging layers is inherently destructive; you always lose data when doing so.