The Mishnah in Ohalos (18:7) which the Gemara here cites is discussing a male gentile. The concern is that he may have brought a Zonah in to the house after the time he moved in, and she became pregnant and miscarried from that time. Thus, the minimum number of days that could have passed so that the embryo could be Metamei is 40 days. (We assume that the Zonah he brings into his new house is a new one, and therefore she will have not been pregnant from him from already before he moved in. And if she miscarries another person's child, he certainly will not bury it in his house.)

Your question applies, though, to a case of a single woman who moved into the house (if a married couple moved in, and she was pregnant before they moved in and miscarried within 40 days of moving in, they have no need to keep it secret and bury it in the floor of the house; a single man or woman who is involved in Znus, though, certainly wants to keep it secret, and so they bury it in the floor). Although we did not find that any of the commentators in Ohalos or in the Tosefta discuss it, it seems that you are correct -- if it was possible that she was pregnant before she moved in, then even if she was there for less than 40 days, we must be Choshesh for Tum'ah. The Mishnah in Ohalos is referring only to when a man moved in.

Y. SHAW