I guess my concern is the bobber stop is pegged so tight to the front of the hook that it's causing some kind of interference with the hook when I set the hook.
That's probably true, but it has nothing to do with using a bobber stopper or a toothpick or whatever the other favorites are. Just pegging the weight right up against the hook is what causes this. It is the difference between the fish having the entire rig, weight and all, in its mouth versus having just the worm and hook.*
Try this: Rig a line with a hook and weight, put the weight against the hook in the palm of your hand, put the line between your finger and thumb, lightly (or tightly if you want) pinch the line in that finger/thumb crotch. Now pull the line to try and pull the weight/hook past your closed thumb. Do the same thing without the weight. Which one has the least resistance?
Note: Don't jerk on that line like you are setting a hook unless you want to next learn hook removal techniques.
I use bobber stoppers to peg. How far away from the hook depends on the situation, but if it is right up against the hook, I just remember I need to set the hook a little harder to get that weight past the fish's lips so I can drive the hook home. If they really eat it and it is further back in the throat, this is not as much of an issue since you have some room to set the hook before the weight is against the back of the lips.
*Yes, a jig would be similar, but the orientation of the line eye kicks the hook to one side or up and catches flesh. These pegged worms are pulling in a straight line.