I think photoprism and photostructure don't really care about your directory structure or organization, but paperless(-ngx, or whatever is the most current iteration) is "notorious" for being opinionated about organization / not wanting to respect your organization.
I used camlistore/perkeep for photos for a while, but google photos has an absolutely killer feature of knowing who is in every picture, even accounting for age: although two of my boys who are 8 years apart look really similar at similar ages, it knows who is who. I don't know if it uses facial analysis or photo metadata or what, but it has never mistaken one for the other. I don't have a reasonable way of getting that tag information out of google photos (even though I'm paying for the service).
It might be time to revisit this, though.. I don't recall whether photostructure / photoprism try to do facial recognition, but even if they don't already, I bet they'll soon be roughly on par with google photos (or good enough that I can stop depending on google for this).
That's documents and photos / videos, what about music? For better or for worse, It's been at least a ~decade since I tried keeping my own music collection as files. Are there things these days like paperless / photoprism, a library system for music that has deeper integration with the content than just "files on disk"?