@jonas My apologies, I meant to follow up on this on GitHub and hadn't found time. I took a look at the code links, I have some background in reading code at least, but I was out of my depth to be honest.
So, I've tried this a couple of different ways. I have the NAS server in the closet, and I can access it on my Linux PC via NFS (which is set up to automount on demand via autofs, and unmount after inactivity), as well as a more traditional SMB. The SMB I have set up to mount in fstab. I've tried setting my full library to one or the other and I do see the same issue via both protocols. Well, with subsequently added folders since changing the mount point results in a new library.
To add some more confusion: I recently shrunk my Linux partition and installed Windows in a dual-boot configuration since I had need for it. I decided to try Strawberry on Windows, accessing the share via SMB. I have it set as a networked drive (M:), and my library is pointed to M:. I do not encounter the issue on Windows -- it seems to add new directories just fine on startup when set to scan for changes.