yes its been done before, you have to search to find the pics of it though. Someone installed a TA hood on a b5 blue srt8 (without a maggie) there was one conflict where it needed to be rigged to fit, i believe the owner melted the plastic on the arm (it was on a leading edge so didn't alter the overall flow of air in the unit itself) to allow the hood to close.
Just like when i decided to alter my CAI to work with the ram air kit, it involved a little cutting on my part, or customization. Should be well within the abilities of most car modders.
My mistake, the b5 blue one was the guy with the maggie. I doubt the intake being too high is the main reason, it doesn't stick higher than the maggie would. If you can install a flat hood on a 6.1 it ought to fit as the underhood box really doesn't sit much deeper than the indent in the hood itself, the arm however does, so if there is going to be a conflict i'd put my money on the arm piece going to the intake.