I'm not so concerned by this. The WY party in Alien 3 is hardly a reliable source of information, as they were clearly going to feed Ripley any line they could in order to get their hands on a specimen. As for Alien Resurrection, Number 08 has blended DNA anyway, so the usual physiological factors aren't going to play out.
In fact, the idea of the chestburster screwing with the host's immunity and physiology accords with the 'viral embryo' fan theory that has done the rounds for years now, ie that the facehugger doesn't deposit a physical embryo, but instead provides the catalyst for some form of microbial/viral which essentially forces the host body to form the embryo from its own tissue. Progressive organ failure would be a plausible side-effect for this kind of 'malignancy' (a term which the WY party actually uses in the Special Edition of Alien 3).