Yes, of course. But, if he were to pay you with a paper check, he has the benefit of having the float time in which to discover and correct (via the stop payment) any mistake he may have made. Do you think employers want to just give up that benefit? Probably not. Therefore, the ACH provides this mechanism to keep them from losing that benefit.
Now, I also recall hearing a few months ago that, since paper checks are now processed electronically, there was some talk of eliminating the paper float; the check would clear the check writer's account when the issuing bank received electronic notification rather than waiting for the paper check to arrive. If that were to happen -- maybe it already did, I don't know -- this 5 days of float would seem to give direct-deposit employers a huge benefit that paper-check-writing employers no longer enjoy.
I would also not have a problem if someone was interested in holding employers to the rules. But they shouldn't be allowed to just snatch your money for any manipulative or vengeful reason they choose. The ACH rules are clear that they do not have that right. But try and get someone to care.