There definitely looks to be an issue, but it really is best to use a longer metal ruler to measure scale length so all the measuring is done in one go. It's a lot more accurate.
I'd get in contact with pit Bull and complain. As this is a custom order with a different scale length it should have been fully checked before being sent out. The best you will get is a money-back offer, but better than nothing.
It looks like there should be enough of a gap between the neck pocket and the neck pickup that you could extend the neck pocket backwards so it meets the neck pickup. You may need to shave a bit off the end of the neck as well to gain an extra couple of mm. Fill the fixing holes in the neck and redrill. If necessary, you can cut out a section of the neck pickup ring to slot the neck into.
If you redrill the bridge holes for the existing bridge, those large post insert holes will then be very close to the edges of the bridge pickup rout. You may not have enough strength in that area (though most of the force on the bridge is downwards). If I was going to move the bridge, rather than the neck, I'd probably change the type to a more vintage ABR-1 style with the 4mm posts that screw directly into the wood, like on an old Les Paul. This still leaves issues, such as what to do with the old post holes, and you'd also need to ground the strings via the tailpiece (as you couldn't do it using the bridge), which involves removing those inserts and drilling a hole into the control cavity with a long thin drill bit.
Moving the neck would be easiest in my view. You could probably do it all with a sharp chisel. Just cut away that section in red, and then take off a bit from the rear end of the neck. The end of the neck will then need to be flat, which is a lot easier to do than try and match a curve.