He may be demonstrating good patrol practices, but he is also demonstrating bad uniforming practices.
Ya, it just depends which matters more, eh? It seems several folks have already pointed out the "breaking the rules" point of view, and no doubt my post will be followed up with several more people accusing me of breaking policy...
Personally, I tend to find adults who act like scouts to be somewhat goofy. It seems to be an odd feature of the American scouting system. I suspect the uniform policy in question was put in place to quietly discourage that sort of behavior. Having said that, learning by example works best from the top down. If the Scoutmaster's goal is to promote patrol cohesiveness, it seems logical to start by having the adults behave like a patrol, including, perhaps, wearing a patrol patch. It all depends - is an imperfect uniform the cost of achieving a working patrol system? I'd tend to say yes, and your scoutmaster seems to think so too. After all, uniforming and patrols are both methods, not aims or ends in themselves, and it's completely normal for a particular troop to favor one over another.
If this really irks you, seeing as how you're a new parent, my advice would be to let this one go, eh? At least for a few months until you know the troop better. Nothing's more frustrating for an experienced SM than a new parent who comes in second guessing their decisions... Instead, ask the SM what you can do to help.