I 100% agree with everything you're saying. Yes, you show you are prepared for the MCAT by doing well on the MCAT, but that requires you to have that prior knowledge to know how to answer the questions correctly.
And now that I recall, my main concern is actually retaking organic chemistry II. I would've had a C-, but because of the pandemic, I had the option to change it to Cr (for credit/pass) — I had to do it to prevent my GPA from decreasing too much. So technically I don't have to retake it anymore, but otherwise, I would have to. However, in order to be better prepared to improve in organic chemistry II, I have to first do better in organic chemistry I (I got a C+), because these courses are cumulative — at least at my college they are. And I know a C+ doesn't make it necessary to retake it, but the grading was heavily curved, so in reality, even though I have a C+, I have to improve myself in this material somehow. I see the best way in doing so is by retaking the class.
I would like to add — even though it's not important in this discussion — that the reason I didn't do well on my first attempt was due to personal difficulties making it very difficult for me to study effectively, but I digress (just something I'll have to explain in my application and interviews).