As others have stated, as long as your mod does not directly relate to any issues you are having, they have no grounds to reject you.
This is just my tin foil hat side, but keep in mind, we don't know if they are keeping records of all the mods you have (from previous visits), so if you come in with some kind of MAF issue, but you take off your aftermarket intake and put the OEM one on, they might call you out on that.