Somehow, this issue went away. I'm not sure which of the following fixed it, but here's what I did:
* Deleted my local replica and the archive files under `~/.unison`
* Uninstalled then reinstalled unison locally (the same version, 2.48.4)
* Added `force = ssh://username@my-remote-server//home` to the config to mirror the remote server
* Once it had synced, I removed the `force` config option and started as usual
Now, for whatever reason and despite the version mismatch, the permissions are working fine.