Again, video game. You're trying to compare the real world with a game when it isn't comparable and if a US soldier just shot a guy walking around for being dressed a certain way there would be issues.
Video Games, those have mechanics.
Also, if you are so sure an american soldier won't shoot you for wearing an ISIS uniform near their base on hostile territory, go ahead and do it. See how it goes. Tell us about it. Better case scenario they throw you into a cell.
Again, it could've been implemented a bit better with some nuance and you're ignoring the very armor you yourself brought up too. This isn't remotely like save warnings at all either. It's a minor issue but an issue nonetheless, you don't have to bend over backwards to defend it.
They have nuance, you are told very clearly what the faction armor does, you are told through story what the dynamics between the two factions are. You are constantly reminded every 2 minutes that you are "Still Dressed as a Member of the NCR". You have to basically go out of your way and start killing members of a faction to get the armor early game, except for Nipton nothing in the main quest path leads you into a Legion encampment, youactually have to go out of your way to get to those in which case si on you to assume the risk. Same as you deciding to walk into the Quarry Junction and finding Deathclaws. Hell Nipton gives you warning with the Bull Flags at the entrance before you are even within range of the Legionaries perception.
In the case of implementing a "faction coloring system" what would it be then? If it has to be something the Legion can Recognize from afar it will also be something the NCR would see so then Recolored NCR armor would turn into Legion armor. Alterntive you want to remove the faction entirely, the faction armor would then logically turn into a deserter armor, which would basically become an enemy armor as you can see from encounters with NCR deserters who are actively escaping and turnning to raiding because they have no other option, and the Legion take as well to deserters as they take to profligates so.... Alternatively, it would turn into a Raider armor and mark youas as someone who stole an uniform from a dead soldier or killed him to get it, again, Enemy Armor.
Unless all you want is to remove cosnequences entirely, by which point that makes the central mechanics redundant and pointless.
The faction system has some issues I would like to see fixed and expanded upon, but this you are complaining about makes zero sense from an In Universe stand point and from a game design one.
DLC armor are a different matter because those were made to be side content not directly related to the main game. It would make sense for the Desert and Riot armors to be seen as faction armor but then you would complain about paying ten dollars and not being able to wear those on Legion territories... so it's all an endless cycle.....