Not sure what this means....
What filesystem will contain the actual amiga files regardless of network protocols in use?
All of them, there's nothing magic about files on Amiga. The problem is meta data, information about the files, the filesystem flags, not the files themselves. A networking filesystem is a network protocol, it's up to the client and server of the protocol to decide what filesystem flags it will present to Amiga DOS. In case the server does not have any understanding of Amiga filesystem flags, the client must translate those to flags that are native to the server, or simply use dedicated meta files on the server for that purpose. Like FS-UAE does with .uaem-files, this has its clear advantages, as it also simplifies rights management/security on the server.