[DaveBlake]

By best advice is don't use cuesheets. They are an out moded approach to digital music from the days when seemless playback was not possible. There is very limited tag support (just the original cuesheet standard). While someone could come along and dream up bespoke additions and try to implement them in Kodi, there is so much other better work they could do I hope that isn't how they choose to sned their skills.

Rip CD as individual music files per track, tag them fully and consistently, and enjoy what Kodi can do now and will be able to do in the future. That includes seemless playback, but also great library support making browsing your collection an enjoyable experience.
 

I'm aiming at being able to do a Kodi search across both folder trees.

No idea what you mean, Kodi does not really care about what folders you use or how they are named. There are advantages to putting all the music files from an album under one folder, after that it is the tagging (of artists, composer, conductor etc. with eventually possible support for work too) that counts.

Just test it out with some of your music - split into separate files per tarck, tag with Picard, scan into Kodi - and see how it works.