None of us can predict what any given AO may do but the scenario you presented makes sense to me. Having the guidance counselor write the note is great because: 1) there is an independent verification and 2) it won’t sound like you are trying to make excuses.
Admission at T20 colleges is difficult for any unhooked applicant. As long as you have a well balanced application list (including match and safety schools that appear affordable and that you would be happy to attend) then you will be fine.
Good luck.