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Since you are talking about Samba I assume you have a Linux VPS acting as the centralized backup server. You can always create mountpoints for Samba shares in your /etc/fstab using the cifs mount type and putting the credentials in a file referenced in the options. For details see this Ubuntu wiki post on mounting Windows shares permanently. At that point your site's root is basically a local path such as /mnt/site1. For all Solo cares, you have a local path. It doesn't need to know anything about the underlying filesystem and the OS won't tell it either. It is blissfully ignorant and works just fine :)

If your site servers are also Linux, however, I'd recommend using NFS instead of Samba for the network shares. It's a much faster protocol and you can definitely limit access only to your server. Please do not try using fish, sshfs or any such end-user-oriented solution; they are fine for the occasional file transfer but suffer horribly for performance when you're trying to access an entire site's files.

Samba is meant to be used for transferring few files, not a large amount of files with random access reads. Your best bet would be NFS with async on both the server and the client since we're only doing reads in our use case and don't care about filesystem consistency.

We basically want both ends to not bother too much with filesystem consistency. The backup assumes that some files may change during its run. We know from experience that this kind of potential inconsistency is tolerable in the context of a site backup. Moreover we want our client (the backup server) to use in-memory caching since we're doing random access reads to essentially the whole file every time. The reason we do random access is to prevent PHP from running out of memory or time. Having the client side use memory caching means the whole file is transferred from the web server's disk to the backup server's memory while our PHP code is compressing the file. To further understand the context of these options please read this first.