Yes, my Denons and my Onkyo all have direct/pure direct, but still have control over the sub beyond that (or with that), altho just on the Denons IIRC, don't think my Onkyo offers that particularly, think just "stereo" mode uses the sub, but I'd have to look again, its been a while since I've gone thru setup on it.
As far as some bass boost, particularly at lower volumes, you might try Yamaha's variable loudness contour feature, think it's called Yamaha Volume or maybe YPAO Volume?