Immich and paperless like their own data structure. But they both also just keep your files pretty much intact.

So in order:

• Since I mostly only use 1 app to manage each “type” of data, I let them have their own folder. Unmanaged files just go on a personal share
• By pretty much just accessing the files trough that application. The only way I need to access them in another way is if I need to migrate to another app
• I don’t use Nextcloud, but when accessing files, doesn’t it just show the normal folder structure? You can give it access to the “base” folder and see everything if needed.
• Two ways: 1. the more important the data, the more mature and hopefully with longer support the app needs to be. Documents and photos are important. Game roms are not. 2. Only choose apps that don’t store the data in a proprietary format. Both paperless and immich like their folder structures and naming, but it’s still pdfs, jpgs and heic underneath. This way of I need to move apps, at most, metadata is lost.
• I just backup all of it — app data, files, etc. No real impact.