I agree, when it comes to the check boxes in that form.
In the “Additional information” section, the GC is allowed up to 500 words to explain how the check-box answers may have been impacted by community-scale disruptions such as COVID-19 or a natural disaster. It also has a bullet for “Other extenuating circumstances” as being appropriate to discuss there, and notes that space is provided on the student’s portion of the application as well for such explanations.
At least at a competitive holistic-admission college, each AO reading the file will digest all of it and arrive at an opinion as to the overall academic suitability of the applicant. At a highly-competitve college, whether a file gets gets selected for championing when the AO’s meet probably won’t much hinge on academic particulars (my opinion, but I have seen a lot of applicants and their admission outcomes). That’s because there are many many more applicants who are quite qualified academically than there are admission slots. The AO will want to see great academics, but a whole lot more. EC’s course, but could also be something(s) which speaks to exceptional character, ability, or leadership (beyond “president of…”).
In my opinion, most admission decisions at highly-selective colleges don’t hinge on a couple of AP classes one way or the other. The overwelming majority of applicants who have all the AP courses one could want will still be denied admission, while others who for whatever reason couldn’t fully load up will be admitted anyway. So just explain your situation, and let the process work.
If you do decide to provide an explanation, do yourself a favor and keep it terse. Nothing about fair/unfair, for example. Note also that if your grades are less than perfect in the equivalent non-AP courses, presumably all of this is moot.