it makes sense to me, the mount looks good and Im sure it sounds great!
Take a good look at the sub enclosure. It's small, puny and pre-internet practically. The best thing you can do is trash it. i think mounting that amp in the rear quarter panel is a great idea. There really is no downside to leaving the other amp in place so long as you're getting the benefits of the system.
I think the installer was nervous about screwing up anything still relying on that amp. It can be removed, but take him at his word, if he doesn't feel comfy, I wouldn't risk it. I take it you just bypassed that amp and only used the amp for the sub?