I would imagine you have a file sync set up between your laptop and desktop. The settings themselves are local to the machine.

If however your user data folder is synced. I dunno the mac path but windows is C:\users\name\documents.

It copies any settings I make from my laptop to my pc but only because I have a sync setup on my users folder so anything I can do on my laptop I can easily continue on my desktop.

Can either disable the sync. Or add an ignore rule for the ffxiv directory within your user data