Maybe a bit late now but personally I'd always fill any remaining gap after gluing. If you are going for a solid finish or a burst that will end up with a solid area over the join, then it's easy to cover up the filler and have a seamless join. If you are using stain and clearcoat, then you'll want to get the filler to match the stain colour as well as possible. I often use acrylic paints (cheap artist acrylic tube sets from Amazon) to tint my filler, though I have also used a coloured Sharpie if it matches the body colour well enough.

But when clamping to glue the neck in, you may well find that 0.5mm gap closes right up, or you just have a hairline gap that the clear coat will fill. Just don't panic; take it easy and see what you have after the neck is in, and take it from there.