"the only primary difference was that one happens before the aggregation and the other happens after, and all the other implications stem from that fact."

This is correct. The biggest implication of that difference is that, when you filter rows via a HAVING clause, the query will first select all the rows and aggregate them, and only then begin to filter them. That can be a massive performance hit if you thought that the filter would prevent filtered rows from ever being selected. Of course this makes perfect sense, there's no logical way to filter an aggregate without first aggregating, but it's not obvious.

"PRQL's simplification, rather than obscuring, seems like a more clear and reasonable way to express that distinction."

My main point is that PRQL makes no distinction. If you didn't inspect that SQL output and already know about the difference between WHERE and HAVING, you would have no idea, because in PRQL they're both just "filter". Hence, PRQL is not simplifying the complexity (you still need to learn the full SQL syntax and the specifics of how it works), but it does obscure (you have no hints that one of your filter statements will behave completely differently from the other).

As far as removing arbitrary SQL features, I agree that that is it's main advantage. However, I think either the developers or else the users of PRQL will discover that far fewer of SQL's complexities are arbitrary than you might first assume.