I would consider flattening the top of the sight, mill or file, AFTER I drilled a hole , either on user side or all the way thru, for specific sized fiber optic rod. I would then continue to whittle away on the top of the slide to expose the prototype rod to some light. Alternatively angle a "ramp" only the back 1/2 of the user side, serrate with file and / or paint with bright color.
Milling / filing a flat for dovetail doesn't look like a viable Plan; pretty thin there.