Hi,
That happens on almost half of my fowling guns because I make them so slim and choose barrels with thick breeches. If the lock bolt only partially blocks the rod, turn a portion of the bolt in the middle thinner. Don't notch it, turn it on all sides so it does not have to always be returned in exactly the same way. If it is an 8-32 bolt, it can be easily reduced to a size 6 bolt stock. That may solve the problem but you have to remember to remove the ramrod before removing the lock bolt. If that is not enough, taper the end of the rod. If your bolt goes right through the middle of the ramrod hole, you may need to do what you originally suggested.
dave