What are the specifics of the concept you have?
I've built dozens between Allparts, Musikraft, Rosser, Saylor Guitars, USA Custom, Warmoth, WD Music, etc. and Warmoth is about as custom as you can get (especially for neck options.) From my experience, they have amazing customer service too. If something is not offered in the drop-down menu options online, just email asking if its something they can do (almost everything I've asked for was available for like a $40-$100 upcharge.
I finish them myself which saves money but Warmoth does offer beautiful finishes that look great and last a long time. Also, never had any issues with a Warmoth neck fitting any Fender body nor any Fender licensed bodies.