Your question tells a different story than your screenshot... You left something important out.
What you're doing is fine, as far as it goes. Having EQ and PEQ both active is also fine. You just need to remember that they have a cumulative effect.
The real problem is that that -6.1db pre-amp cut figure is meaningless by itself.
You headphones have a specific sensitivity, and that means they output a certain volume level at a particular voltage. If you do not know the voltage output of your headphone jack, then your -6.1db is meaningless.
So for example that -6.1db might be correct for a headphone jack at 0.7v RMS, but it will be totally wrong (not enough adjustment) if your voltage is 0.9v RMS, or (too much adjustment) if your headphone jack is at 0.55v RMS.
So unless you have the equipment to measure the voltage on your headphone jack, stop wasting your time and adjust the level to where it sounds good. Because any volume (pre-amp) adjustment you set in the PEQ or EQ is totally irrelevant as soon as you touch the volume control in MC, or your DAC, or your Headphone Amp.
Looking at the rest of the stuff in your screenshot, the real story appears: it seems they also gave you specific boosts and cuts for different frequencies. The only reason they are recommending a -6.1db adjustment is to make room for the 6.5db boost they are telling you to apply at 4600Hz. When you're boosting that much, you'll need to lower the overall volume so you don't clip.