I had the same fenders with some toe overlap. Instant gonzo to the front one.
That bit of wire showing is no big deal for me, it is on the rack after all. Mine is way worse.
Putting holes in the fork or frame is just a bad idea. IMO
As for custom, I doubt they would change the fit much. It looks just fine to me. Maybe the stem could be shortened and TT lengthened.
Switching the wheel and shifter to or from a Rohloff would be no problem.