Ah, ok, that makes sense. However it also results in the usual chicken and egg problem of not having the ignores available until after the folder has synced. I guess this is fine in your case if the ignores are always symmetrical. Regardless, it sounds like imsodins suggestion would be helpful.
Just set up a new laptop; synced my files from my NAS; made sure everything was sync’ed correctly, all looks good. A week later, I notice there’s some weirdness where files that are in my ignore list aren’t being ignored… guess what I forgot to enable AGAIN? T_T