That neck plate issue is common on the bolt on kits. A strat I am building for a friend had the same issue, as well as the body holes being in a slight rhombus shape rather than a rectangular pattern.
My OCD couldn't deal so the Body end got squared off, and the through holes got filled and re-drilled to match the plate.
I also went up a 1/64" in drill size on the new holes to clear the screws properly when it is tightened together.