It sounds like you are trying to fit the neck too far into the body. The end of the tenon does not sit right against the rear of the neck pickup rout (though I know it looks like it should). When you glue it on, position the neck so that the end of the fretboard is just forward of the pickup cavity, so that you can get maybe 0.5mm of pickup ring sitting on the edge of the rout, just enough so you cant see a gap under the pickup ring.

I've done that on all my set-neck guitar kits where the neck pocket and neck pickup rout are all one, and haven't had had any intonation issues.

On my EX-1, the neck pickup ring is just resting on the front edge of the pickup rout, and you can't see into the rout.