It is likely that the non-opioid portion of the kratom effects would still be felt, though it is subtle at best, when on bupe. It will not cause PWD though, bupe causes PWD when you're addicted to something else and take it. If you take something on top of bupe, it can't cause PWD, it will just not work at all, or only work a tiny bit.
And actually, if you're addicted to kratom and take bupe, it also won't cause PWD like it does with other opioids. This is, I believe, because kratom and bupe are both partial agonists. So the bupe indeed kicks the kratom alkaloids out of the receptors, but since bupe and kratom are both partial agonists, it will fully substitute for the kratom and you won't get sick (in fact I prefer bupe's high to kratom's)