Small-scale infestations have always been possible in the main complex under certain conditions, they're just fairly rare. That said, the point has always been to keep the complex relatively predictable, so not too much special area RNG or wild adjustments. That's why there are almost no special rooms like those seen in branches. As we've discussed I'll consider adding more, but am moving slowly on that since I'd prefer to make the branches more interesting instead, as they're more flexible. The Beta 4 Materials update does make some significant changes, though... the first to the main complex in a long while.