I'm not sure I have specific advice for you, but I do have a couple comments on algebra 2 which might help you in how you approach the decision.
My DD 16 just finished honors algebra 2, which I assume would be the same as pre-AP? (We don't have any pre-AP classes, but do have honors, which generally cover more material and at a faster pace than the regular leave ("regents level" here) classes,)
This year, at our school, was the first year the algebra 2 class was a common core class, and the material it covered differed significantly from the previously offered algebra 2 course. It differed so much so that although kids are allowed to take both the old regents exam and the new common core exam at the end of the class, and can choose the higher of the two grades, the math department strongly advised against taking the old exam- the kids did not learn much of that material. The new common core class algebra 2 contained a lot of statistics (one teacher said it was about half the material covered in AP stats), much less trig, more in the way of sequences and series. Those are the main differences I remember, but you may want to look into the topics covered in more detail. Also becuase of this, next year's pre-calculus class, though not common core, will also contain a lot of different material, I assume to fill in things not in algebra 2 (word is that a lot of the trig will end up here.) Again, so different that the math Dept here is not accepting any summer pre-calc courses done at local colleges- they just don't cover enough of the same things,
I think it's strange (and unfortunate) that your school has such rigid pre-requisites- I would think that your son has demonstrated that he should be allowed to take a higher level math class. Here, there are guidelines, but any kid can get a parental override and take honors classes; if the pace is too much, kids drop down to the lower level. There were at least 3-4 kids in my DDs class who dropped down, as the pace and volume of material were a step up from even honors geometry, but at least they had the chance to try. And yes, this approach does lead to weaker students struggling and using tutors to keep up, but again, it doesn't limit the opportunities of kids who want to take on more challenge.
As far as content in honors geometry vs. "regular" that might be missing- at least here, I think the main difference is the approach. Our honors course expects a lot of proofs, and my sense (no experience here ) of the regular class is that the proofs are much more simple, more rote, if that makes sense. I think honors kids also spent more time on constructions. Regardless, I would think that algebra 1 exposure would be more relevant to the algebra 2 material, but that's just my impression.
(Just a caveat- I have limited knowledge of much of the math material here recently, becuase my kids rarely if ever need help and i am consequently pretty uninvolved, so take my musings with a grain of salt!)
