I fail to see your point. If you use trans-am for an extended period of time (this might very well be a number straight from the script writer's hat suiting each scene individually), the suit will drop out of trans-am and can't perform for a while until the genuine GN drive has reached some critical particle density again. However, if you use trans-am for a few seconds to quickly get somewhere, there is no imaginable reason why you couldn't drop out of it willingly and still easily possess enough particle density to fight normally. In fact, any sensible pilot would do that if there's a risk enemies still remain around. Even more so if you are flying with a fake GN drive with no regeneration ability.

Trans-am is, fortunately, one of the aspect of this show that is not 100% tied to metaphysics, so I don't see why it can't be used in an intelligent and systematic manner. All in all the general trend right from the beginning has been to have new technological gimmicks in each successive battle. Trans-am is already an old trick in the show, so why worship it anymore?