How do we explain the machlokes if a lady becomes pregnant near the time of her vest or the time of her tvila? Definitly the opinion of somuch l'yom havest seems problematic but also the opinion of somuch l'tvila if it's refering to after 7 days of nidus (I'm not sure if their all were machmir on Shivah n'kiyim for a regular niddah).
This Machlokes is a Machlokes Amora'im between Rebbi Ami and Rebbi Yochanan (Nidah 31b) and therefore it is safe to say that Rebbi Yochanan's position of Samuch l'Tevilah is based on the Rabbinic requirement to count Shiv'ah Neki'im. This is based on the fact that already in Rebbi Yochanan's time the Mesorah for ruling on all the various kinds of blood had been lost, which necessitated the Gezeirah of Shiv'ah Neki'im (see Nidah 20b and the Rif on Shavuos 3b).
Understanding Rebbi Ami's position - Samuch l'Vestah - is indeed difficult in light of our understanding today of the menstural cycle. We understand that by the time the Veses comes, the woman is long past her period of fertility.
Rav Dovid Karlin (She'eilas David, 1) says that in the case of a Machlokes Chachamim about the physical nature of things, the Chachmei ha'Teva can be used to decide in favor of one side or another (if, however, there is no Machlokes Chachamim - for example on the issue of Chidush ha'Olam - then we must follow our Torah tradition despite it being at odds with the view of the Chachmei ha'Teva).
This is not a Psak Halachah