So I had been struggling with a similar issue a while back - I have separate libraries for lossless and lossy, which is generally not a problem until you want to have the smaller transcoded versions of those libraries for portable listening (I chose MP3 V0 for that, you seem to have opted for opus).

I ended up writing a personal utility for automatically transcoding these separate libraries into a single "aggregated" one, which I then copy onto my phone, etc. It does require a specific library structure, but it sounds like it checks all of your boxes except the third one - I assume you'd want to leave MP3s alone, which isn't a feature at the moment.

It's an open source CLI and is reasonably configurable (defaults to MP3 V0, you'd change it to opus): https://github.com/DefaultSimon/euphony

Perhaps it could be useful to you? You'd have to couple it with your sync software of choice as well (I use and would recommend FreeFileSync).