Dupes Ignore "Vacancy Only" In Exosuit Checkpoints

I think based on what you've described that dupes are behaving as designed... the Clearance setting applies only to returning dupes (going from "outside" to "inside"), dupes that are wearing a suit already may always cross a checkpoint in the "out" direction.

One of the reasons for this is that if a dupe finds themselves standing in front of a checkpoint they always need to be allowed to move in one direction or another, otherwise they will be stuck. Unsuited dupes can always go "inside", suited dupes can always go "outside". To prevent either would result in dupes getting stuck at a checkpoint unable to move in any direction.