Thalāthah determines the number three. The interpretation of qurūʾ has been disputed between menstrual periods and periods of purity. The count and the nature of the counted period are therefore separate questions.
A disagreement about “qurūʾ” does not by itself make the number three uncertain. Confusing these questions would erase the very distinction the rule of khāṣṣ is meant to establish.
A definite indication on one component of a legal text does not mean that every detail of the full legal issue has already been settled.