I still use AFP on my NAS for a few reasons:
1. When I benchmarked it, AFP was significantly faster than SMB. Both with SMB2 and SMB3. Even when transport encryption was turned off.
2. On SMB2+, symlinks created by the client are not real symlinks. They're "Minshall+French" links which only look like symlinks to other SMB2+ clients. To the server and NFS mounts they look like flat files with the target path encoded in them.
3. It exposes a different precision for certain timestamps. Software that uses this metadata to decide whether a file needs to be updated will see almost every file as needing a resync.
It's been a year or two since I checked the status of these. The situation may have improved since last I looked.
Yeah I recently migrated my NAS and took the opportunity to switch from AFP to SMB for my Time Machine backups. There were so many problems like the ones you describe that I gave up and went back to AFP. Looks like I'm going to be forced to spend a weekend with Claude figuring this out.