That's great that you provided examples but makes difficult to quote:)
1. "Transparency on top of terrain features". I didn't quite understand what this means, sorry.
2. "Multilevel breaks transparency". This should definitely work, I'll check.
3. "Contaminants cancel overrides". Do contaminants change tile symbol? I thought they just changed colour, in which case I'm not sure why it breaks overrides.
4. "Transparency in workshops". Workshop transparency is currently disabled. I think the reason for this was that I tried playing with it enabled and it was very very difficult to notice workshops on the grass. Of course it depends on tileset used and workshop type, but I thought it would be better to not make changes to workshop rendering at all rather than make it worse. Also, I sort of would expect workshops in RL to not be just objects placed on the ground and to have if not flooring but at least something which would make workshop tiles in game in turn have their own background. So we need some decision here or a way for tileset authors to control this (and I guess for some other types of buildings too, stockpiles maybe).
5. "Items on slopes". This is strange, I'll check it.
Can you upload the save you used to make these screenshots, including raw folder and art/init folders?
The limits question is more important. There's no fixed number, it depends on graphics card used. I think all currently used cards should support texture size 4096x4096 or at least 2048x2048. This gives 64 512x512 sheets or at least 16 sheets. It may seem ok then, but this also includes all creature graphics, so I really need to find a way to split tiles into several GPU textures and not worry about limits anymore.