I concur, I lived the one sub then two subs scenario and yes I had deep bass from two big subs but did not sound like natural bass. Shopping for speakers I met Duke and got his speakers, I have to say the sub array was an extra on the purchase as I wasn't looking for subs I had doubts honestly the Dayton sub amps (because of the price) will integrate and control the subs properly, I looked into more complex sub integration like mini dsp, dspeaker, trinnov etc but with digital dsp comes a side effect within the digital world which is losses during conversion if you are using hires content, anyway the subs arrived, I installed the them and was very surprised how well Duke's approach worked, I sold my two big subs and never looked back. The sub array takes almost no space as a matter of fact less space than my previous 2 subs and I have 4 now, can be easily positioned anywhere and the sound is natural bass not boomy, the daytons will provide all the phase controls and analog corrections needed, the price for the entire 4 sub system is the same or maybe a little less than the 2 subs.
Keeping this on thread for the OP the 4 sub approach allows you to put the subs almost anywhere and makes the positioning simpler and more inline with the geometry, because of the reasons already explained above by Duke himself, some others here are using 6. The daytons allows you to change the phase gradually not only 0 and 180 that is something digital sub integration usually don't have and I think not because is hard to do but the manufacturers haven't seen a need for it, I say usually because the high end ones trinnov comes to mind have it but be ready to hurt your wallet.