I don't know anything about M-L's ARC system; however, I believe it is a safe practice to make things as good as you can before running the ARC.
If you feel the need to eliminate the bass traps and coherence treatments, you can try running it without them, but I think it is better to actually fix the room than to fix the signal. Bass traps fix the room and ARC attempts to "fix" the room by altering the signal! I think ARC can make valid improvements, but I would not consider it the first resort if you can accommodate treatments!