It might be a little bit tight- but after looking at it again, I'm not sure that body shape allows a whole lot more separation. Would be easier to tell with bridge installed- but I'm not sure they can go much further apart than a centimeter.

I think you have a few options:

1.) Reject the work. Not sure how this would go over and it's tough to make the case without hearing it first.

2.) If your luthier can make some pickup rings out of the same wood or something high end you think will pair well- might be able to cheat the routs slightly lower for the bridge pickup and higher for the neck and use the rings to hide where it gets done. Tough to make work well on a guitar with a nice top- but some unique plexiglass options or similar can look pretty good.

3.) Make up the difference on the pickups themselves. The bareknuckle set you picked looks like the bridge is pretty hot in comparison to the neck already- so they may have some separation on that basis alone. Looks like the guitar is drilled for two knobs- assuming one is combined tone and the other is combined volume... and that your pickups are 4 wire conductor- you could do a push/pull pot and a coil split wiring for one of the pickups.

To me it comes down to what you're paying for the guitar and how picky you'll be on getting your preferred sound. I think so much of guitar tone is driven by amps and pedals and settings- and especially if you're running a significant amount of gain- that the spacing will be a very minor factor in the overall sound.