Gosh, @toscala, I don’t know. If the rest of the rec is well-written and well-supported with information about your abilities as a student then maybe the best thing to do is not to call any additional attention to it by bringing it up elsewhere. Hopefully the colleges will just gloss over it when reading the rest of your application.
Your mom/counselor can’t be the only homeschooling parent that’s ever written something “different” from what the colleges are expecting to receive in the rec form. I can’t see how they would hold it against you since it’s out of your control.
Good luck -