Enable audio in Media Replacement mogrt's

Is it possible that media replacement can work with the audio in that media which is being replaced? Maybe I'm missing something but how could we approach this situation:

For instance, we have video clip number one (of a variable length), which has a complex transition built in after effects, that goes to clip 2, which is also of variable length and can also be replaced. Instead of a protected in & out region, you kind of create a protected 'center' region, which is the AE transition, and the in & out is the footage itself in Premiere.

Now, for even a simple positional slide-in of footage to match my wipe animation from AE, I'd have to use an extra adjustment layer in Premiere, matching the speed of my mogrt.