I quite like the idea of those side effects they would raise the skill cap of the team working together like a well oiled machine and I don't see a problem with that.
Provided the alterations do their intended task and make the gunner more effective at his job, so more builds work optimally with the 2 engineers and a gunner set up, rather than the 3 engineers, which I see very often.
3 engineer builds would still be viable and perhaps even more powerful than the 2 engineers and a gunner but only if there was some hardcore team orientation in it.