I am developing an open-source DAW with Qt (https://ossia.io), to solve the problem you mentioned I used AppImage with great success - of course you have to ship all your libs, but that's what you have to do on macOS and Windows too anyways.
I used to but I'm switching to a different model
> Do you do a separate AppImage for each plugin?
no, they are just loaded as .so / .dll / .dylib in the ~/Documents/score/addons folder. They can't have further dependencies though.