^^^Agreed, and it'd be easier to believe Chapel was able to create their disguises based on visual date procured by the Archer crew. That she was able to duplicate the appearance of a species they had yet to study closely on a genetic level was a bit of a stretch.
I guess you missed the dialogue where M'Benaga she's a civilian on loan and part of a project (IE - the method they just used in this episode to 'blend in' with the natives') basically pilot-testing this new 'Altering Genome' approach to see how well it works. She's not a member of Star Fleet proper at this point and time.