Ok. I drawn the layout some months ago, but probably I didn't analyze the schematic, so I did it now.
The bass response that dirtybogner hears is indeed a little hump around the 125Hz caused by the transistor eq gyrator, this hump is noticeable even when the bass switches are closed (or the Bass pot are at zero). The switches cut off some db but not soo much. This feature is reported in the description of the pedal on the Xotic web site: the min boost is 2.4db, the max 6db. It's always boosted a bit.
To remove totally the 125Hz bass hump we have to jumper the 18k R6 resistor. Actually, doing this we could lost something more of 1db of overall gain, but I have doubt we can hear it.
Using simply a 2.2nF as input cap like the new switch added by dirtybogner, though the cap value is reduced drastically, the low cut is in the very low frequencies. I expect we can hear it, but not so much.
And, about the bass pot that replaces the switches, though is a good idea, that is a control of that db range of the 125Hz, exactly how the switch does, but just we can do it with a pot.
I build pedals