I meant to jump in sooner but I had to crack some books on this one.
Two things going in:
1. Superposition holds.
2. Standing wave room modes are independent of sub location.

Superposition is important because it basically means that the response of the sum is simply the sum of the individual responses. Where it get complicated is that the output of the sub has elements of Amplitude, Frequecy and Phase and most EQ programs only show frequency and amplitude and maybe a phase shift and give you no idea what the absolute phase is (Never played with Sub EQ HT).

The room modes are important because adding extra subs will not change the room modes. What it will do is move the peaks and valleys of the standing waves around. Note the same effect is achieved moving a single sub around in the room: The modes are the same, peaks and valley move. (Opening door, moving walls, etc. WILL change the room modes)

So what I would do if I were designing the system would be to measure the individual sub responses AND the combined response then apply individual corrections to each sub to equalize the combined response.