I'd not worry about seeing the scarf joint either. Original rickenbackers don't have it as the headstock is parallel with the fretboard.
Re gluing the neck, someone on here just put glue on the bottom of the tongue, and the tension in the neck bowed the back of the body slightly, if you get it on the sides and heel too the extra contact surface seems to be a good idea. Mine has not done this. It is a small glue area on these kits.