The thing with any equalizer and adding/reducing any frequency gains is that it will remove the peak/dip at one frequency at a point in room but will add it somewhere else. That's the hard fact. The best way to take of boundary gains or any peaks dips is trying different sub placements till its gone, use multiple subs and or move the sub very close to the listening position (so that you hear the sub first directly before the room hears and throws the reflections back). Trying to equalize it will only do it for the position where the measurements are taken. Adding multiple subs (ideally 4, each at the center of the room) takes care of most of the peaks/dips and improves seat to seat consistency. It still may not be accurate freq response, but it will still be consistent from one seat to another. Now, having multiple subs is not ideal for all, because of the room limitation, aesthetics and budget.
That's where the eq comes into picture. Fortunately, I have only two seats in the theater room, so it wasn't that bad. If one has to do proper equalization, then best way is to measure the room response at each of the seat or at the positions more important to the listening area. Superimpose those and try to get an average room response. Try to equalize to get that curve as flat as possible.
But you are right - Eq is a double edged sword. It can easily make or break things. What's more, it can work very fine in one room and in another it may not improve things at all. Best way is like what you did. see if it works, if it doesn't, remove out of the equation.