Why do they recommend turning the EQ OFF before setting gains?

Doesn't the voltage being pushed through the HU\Amp go up once you start adjusting the EQ upwards (like bass)? For example...I used to use the "Rock" preset on my HU. When I set my gains, I followed the guide as it was written, and thought nothing of it. I didn't put the EQ setting back on, because I thought that it would throw off all the work I just did, since it boosts the bass volume considerably, therefor upping the voltage (At least on the HU's end) past what I had already set as the max.

Another example is the MX setting. With it off, the preout voltages don't hit 4v until volume 35. With it on, they hit it at 25, and badly distort if I go higher! So if I turned off MX and adjusted the gains, and then put on MX, I would have blown my speakers.

There must be some reason for turning EQ off before setting gains, but I guess I'm missing it