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Normal foundations can have some varying breeding quality, even if all yellow papered. I don't know if its a significant amount.

I wanted to note that AFPT (average foal PT) does take into account the sire you are using, as the sire also affects the PT score of the foal.

So if you send 10 mares to a C stud and 10 mares to a B stud, the mares who went to the B stud will generally have a better AFPT.

I know the breeding abilities have changed recently and im not sure what still counts or doesnt. All horses have a hidden number on how well they produce an offspring . You could take the ten yellow mares and 5 could have higher pt foals where the other five may have lower or the same pt score as the parent. However the higher pt doesnt mean itll pass breeding inspection or even the lower pt foals could produce better pt foals down the road. Stallions play a part to. Used to find that certain stallions paired up better with certain mares vs others but i think that is something that has changed. I beleive it is now a range based on the parents and luck.