It's not gonna matter except for looks, as long as it goes in Tight & won't move. After ya get the barrel & everything browned & back together, take a little KIWI Brown paste shoe polish & pack some under the sight, wipe off excess & forget it.
2nd option is cut a piece of metal to fit & fill the dovetail & file flush. Move down the barrel 3/4" & cut a new dovetail & start over.
3rd option is to file of the rear sight a bit to make the male part of the dovetail go deeper. This is prob what I would do.
If this lil glitch is all the issues you have, you have you are in good shape.
Once ya have the sights fitted, take them back off. Just something to snag your hand while building the rifle.
You won't need them again until you assemble the rifle after it is all blued or browned.