That scenario works because the response of the subwoofer doesn't change due to interacting with another subwoofer. Not a question of better or worse, but what is being EQ'd. If you EQ each subwoofer independently, when they'll never be heard that way, then you're EQing the wrong thing (and wasting your time). That would be like EQing a subwoofer in the middle of the room, where it is easier to get a flatter response, then placing it in the corner where it is going to reside before EQing it again. Why bother with the first round of EQing when no one is going to hear the sub from the middle of the room? Likewise, why EQ each sub independently when no one will ever hear it that way. Why is it more difficult? You measure the bass response, and minimize the peaks and dips as best you can. What difference does it make how many subs are physically connected to the EQ? That uniformity disappears the moment you turn on both subwoofers. Try it for yourself and see.