If it is not hitting the lockbolt dead on square in the middle, you might be able to take care of it by tapering the last part of the ramrod and turning a shallow groove all the way around the center of bolt - that way it does not matter if you remove the bolt with the ramrod in place or not.
(Correction - I wasn't thinking - it would matter - you could not pull the bolt through in this case for removal, but at least you would not have to worry about aligning the bolt groove with the rod, as described in the next option)
That being said, if you want to just file a notch on the side of the bolt where the rod hits, just put a mark on same side of the bolt head that the notch is on, so you can see where to align it to allow the ramrod to pass by. I have seen originals built this way.
Or, as the others have said, don't worry about the front nail being a bolt and use a dummy screw. I have flint guns with a single lockbolt that I have been shooting for many years, no problems.
Guy