Regarding your question, this may be something you need to check with the adcom. However, if the fact that you took an algebra-based physics class were indeed a problem with the HST side of things, they probably wouldn't have extended an II. Granted, one of my schools gave me an II even though I didn't satisfy the course and letter writer requirements, and they did not alert me of these issues until like a month after the II.
Also, do double-check that your physics class is officially algebra-based. I say this because, at my university, there are 2 year-long physics tracks. The first track is sometimes known as "algebra-based" because it doesn't really use calculus and is pretty chill. The second track is your traditional "calculus-based" series because it's far more intense and actually has a bunch of calculus. However, both classes are officially designated as "calculus-based."