At the beginning of DS9, it was clearly the destinction between starship and starbase personnel.
We saw a lot of starbase personnel on TNG, always with the standard TNG uniform. Maybe I'm wrong, but until "Generations," I don't recall ever seeing any non-DS9 guest star in the DS9 uniform.
It was clearly a distinction of some kind, you're right. Maybe it was the uniform not for all starbases, but for the Deep Space stations.
While I wasn't crazy about the uniform change to the FC gray tops, it did allow for a really great WTF! moment, when we find out Bashir has been replaced by a Changeling and the real Bashir is still wearing the old uniform.