I think you can keep doing the SMB shares and use an overlay filesystem on top of those to basically stack them on top of each other, so that server1/dir1/file1.txt and server2/dir1/file2.txt and server3/dir1/file3.txt all show up in the same folder. I’m not sure how happy that is when one of the servers just isn’t there though.

Other than that you probably need some kind of fancy FUSE application to fake a filesystem that works the way you want. Maybe some kind of FUES-over-Git-Annex system exists that could do it already?