Whether the the sub fires front or down, there is still a direct radiated wave that hits you before the room-affected wave.

When you attenuate a frequency band that is peaked because of a room mode, you attenuate the direct radiated wave.

This allows the room affected wave to dominate what you hear, as the direct radiated wave is attenuated well below listening level.

So, what you hear at listening level is delayed by the distance disparity of the the sub placement vs. the mains, by the DSP of the PEQ and by the room mode.

You may play a ruler flat line, but what you're hearing is grossly time-smeared (which doesn't show up in the graph) in relation to the rest of the speakers, which changes the kick drum from a 'tock' to a 'thhwock'

If you draw a circle around the LP so that every point on that circle is equidistant to the LP with the mains, and use that line as the possible placement options for the sub (+/-) 1 or 2 feet, you have the start of accurate sub integration.

If you then chart the mains without the sub, so that you can determine the in-room slope of their roll-off, after the HP filter, then shut the mains off and do the same for the sub, you can tweak the slopes to resemble a proper crossover...that's step #2.

Tweaking the phase comes next, to fine tune time arrival to your ears of the sub + mains.

This is followed by level calibration, at the crossover point. If the sub and mains aren't exactly the same volume at the crossover point...there goes your entire 2 octaves of crossover region.

Many times, IMO, a dip and/or a peak are mistaken for room modes, when in fact, they are mismatched crossover slopes and badly out of phase sub/mains in the crossover region (which stretches from 30ish to 200 Hz. Run several graphs with the only difference being a 20 degree change in phase of the sub each graph and see how wide a bandwidth is affected).

I believe this because I'm +/-3dB from 15-30 Hz., and +/- 2dB from 30 to 200 Hz., with NO EQ. And, I assure you that my room isn't some magic size and shape.

Maybe I was lucky, but it sure sounds good, and that's always convincing evidence.