Is room shape and treatment still important for four sub setup?
Sure, because bass isn't limited to the subwoofer region, where you have the luxury of using multiple mono signals AND moving tranducers around the room to improve results. That flexibility isn't an option above the crossover point, so how do you address bass problems above, say, 70/80/90 Hz? You're not going to destroy the front soundstage or surround field by moving your speakers to optimal low frequency locations in the room. So this is where room shape and treatments remain useful. What you can't accomplish with room design and bass trapping can then be address with EQ as the finishing touch.
My processor is Lexicon MC 12 and it has L, R and C sub out with individual cross over.
Just a quick correction to that statement, the Lexicon MC-12 has a Left and Right mono sub out which can be combined to run in stereo plus a dedicated LFE out. You are correct that it has 3 outputs but it doesn't have a center sub out, that's the LFE output and it only carries the .1 signal if it exsists in the source. If there is no .1 in the signal the LFE output is silent.