Cbc is a good idea (as would be just using folders inside cbz to create a toc), but I think only calibre uses it and only very few readers can work with cbz's inside cbz's. Unfortunately "comic formats" are in no way standardized and really only zip files with a fancy ending. For metadata inside comic files, comicracks way is the most common, simply because comicrack is the most used software for comics (storing metadata in the zip comment is in my opinion better than comicracks way, but apart from calibre seldom used). To be true, if you just use calibre for everything comic related, embeding metadata into the comics is not that useful, since only a few apps even use this. The other way is more usefull, to get metadata into calibre in the first place.
Polishing cbz is not possible, that's what my plugin is for (but few readers read the information anyway).
If calibre makes a zip on conversion, you can use my addon to make a cbz out of it (it's just a rename). It can convert zips, rars and cbrs into cbz.
Unfortunately I can't help with ios, since I don't know anything about it
But cc can filter quite nicely, so only using one library shouldn't be that big of an issue hopefully.