You could do it that way, easily.
Doing subs in REW AFTER Audyssey could have the effect of timing the speakers to the subs incorrectly because the two apps (Rew and Audy) handle timing a bit differently.
You could manually adjust the sub PEQ by ear inside the miniDSP app as a final step, but Audyssey in most cases after calibrating in multi-X many people engage DEQ.
DEQ in the AVR would not know you added or removed bass downstream in the 2x4 (post AVR.)
DEQ can be super helpful to translate all your tunings in X to lower listening levels for night viewing or saving your goodwill with neighbors/partners
Also the 2x4 would only “ear match” PEQ to DEQ at one listening level, so if you pump the sub bass for movies in miniD, and turn down the AVR listening level, (with DEQ ON), you’d be priming the pump for a souring of neighborly goodwill.
Why? AVR DEQ would add more compensatory bass at lower levels, while miniD was adding even more action movie level bass from the manual PEQ tweaking.
I now compromise a different way— too long for friendly posting length. More info available, though.