Both bolts have the same length shank, as indicated in this photo:
Measurement was taken just behind the head of the bolt, and is measured to the end of the shank. However when both bolts are fully tightened the hammer bolt is substantially shorter. As in, it sticks out from the bottom of the marker less than the guide/feed bolt does.
What may also be an issue is a bit of play in the feedtube. I'm not sure how much it is supposed to have, but i can wiggle the feed just a hair when the marker is fully assembled. Since this serves as the pump guide it does of course affect the angle of the cocking rod as a result. So it would be possible to either catch the hammer bolt head or not depending upon if you were twisting the pump back a hair when you cocked the marker or not. (thus tilting the feedtube closer to the barrel than parallel, and making the cocking rod angle downwards a hair as a result)
Sorry if that paragraph makes no sense.