No, I don’t think this is OK.
If you had mental health challenges during the year, your guidance counselor should address it in their LOR, not you…
If you took college classes, you need to submit those transcripts. Colleges will see your grades from the Rice and MIT courses and make their own assessment.
IMO, this sentence would be a big red flag to colleges: " I also had a hard time adapting to my teacher’s teaching style as the tests would focus on topics we hadn’t learned yet." You are going to be tested in college on topics not covered in class. You are going to need to take the information and apply it to novel problems/questions. It sounds like this “bad” teacher is really just preparing you for what to expect in college.