The Rambam (Sanhedrin 16:6) explains that when we require 2 witnesses for malkus, it is only for the act of the aveirah that we require it. But, the issur itself such as the status of the meat being assur can be established even through an eid echad. Based on this the Chasam Sofer (cited in pischei teshuva Even Haezer 169:13) rules that even if witnesses verify the age of someone to be 13 based on the father being machzik the child as a 13 year old (for example, he was wearing tefillin for a few months), it is sufficient for dinei Torah to assume that he is old enough to do chalitzah. The Chasam sofer argues that if we reject the Rambam's assumption that we can uses chazakos that were established prior to the situation at hand, we would never be able to be mechayev someone for having relations with a nida, because the witnesses would certainly not know that she is a nida (they would presumably only witness the act of bi'ah).
The Pischei Teshuva asks, that this seems to contradict the Shulchan Aruch (Even Haezer 169:11) in the context of chalitzah who says that the age of the child has to be established based on neighbors who know his status completely independent of the father. Why would we require that their knowledge be independent of the father?
It seems from rashi in our sugya that he also assumes not like the Rambam. Rashi writes that if she is machzik herself as a married woman by saying that she received kiddushin herself, and then she committed adultery in the presence of witnesses, she is not stoned. Rashi writes:
ואף על פי שהחזיקה עצמה קודם הזנות בחזקת ארוסה
Even though it may be true that we have a gezeiras hakasuv giving ne'emanus to the father, and we have no pasuk giving ne'emanus to her. Why should he being machzik herself as a married woman be any worse than another chazaka that is established prior to the violation, where we rely on the chazaka and don't require witnesses?