I think that a gauss round should, at the very least, lose its AP qualities if it is incendiary. I agree that the rules, as written, are often guidelines, but players have these resources, and while a good player may appreciate a referee's ruling, some will feel like it is just arbitrariness.
Traveller has a history of being a very specific and technical game when it comes to weapons and hardware. This latest set of rules tends to favor the general and ease of play more. It is when we hit these overlaps where rules as written meet our natural inclination to make sense of the technology that we have tension.
Personally, I think that gauss incendiary rounds should probably not be a thing; they are just too narrow a caliber, and that they are already armor piercing.