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Ammit has said before that the breeding quality of a foundation does not relate to their pt score, if they’ve passed strict breeding advice then they are good breeding stock so if they are what you want to breed colour wise keep them.

BA and SBA compare the breeding ability to both sire and dam, so a high papered stallion bred to a low papered mare will likely have most of the foals neutered, since the mare won't be able to contribute enough ability to the foal to make it even almost as good as the sire. This can give you lots of moderately high PT show horses, and is good for eventually raising your showing bonus. I'm currently doing that in my primary pasture. I have two star stallions there along with a bunch of red and yellow papered mares. The foals all get neutered, but they have very nice PT scores.

Also, a foundation mare with a very low PT score can still be a top-notch brood mare, despite her lack of showing ability. The same thing would apply to stallions.