Our DD basically did that same skip, but went directly into Honors Algebra 1 and completed it in a year. Here are my thoughts: I wouldn't worry about the holes/gaps, if there even are any (based on his ERB there aren't). DD has some gaps in pre-algebra but understood algebra 1 really well and got high 90s on everything she did. In fact, her use of some of the pre-algebra skills that she was missing to solve algebra questions has improved her overall math ability (it is not her strong suit relative to her other subjects). I would not think that doing the course in 2 years would be a good fit however, the pace will be ridiculously slow and probably not challenging at all. I would push for placement into the 1 year algebra class with the skip of the other stuff. DD's entire attitude towards math changed after seeing that math could be more interesting than the pre-algebra stuff and be more interesting.
As far as differentiation goes - it is too bad that the teacher doesn't know how to do it better because it is much easier to do with small classes than with large ones.
Good luck!