Yes.
The rubber feed is there not only to absorb the abuse from the pop bumper, but also as you noted to encourage some bounciness to toss the ball towards the upper PF exits. (If you couldn't lose the ball from the upper PF the game would never end. See black knight 2000!)
But to adjust it you need to either get the ramp metal up, the posts down, or the rubber thinner. Some filling and redrilling of holes may be required, I forget if those posts are machine threaded screws into Tnuts or not. It's been however long CPR make black knight playfields that I've had mine apart, but I know that I made sure of this transistional area (I always do this on PF swaps regardless of title) being spot on.
Yours looks pretty extreme, you might be able to change the posts to the thinner style to shave the clearance you need..... but the other end has to feed that left flipper, too, so looks like some experimentation is needed to get this right.