to do this on a table saw is very easy . Just do it while stock for the neck is all square still. you could do it with one saw blade or with a dado bade and shims to get it done in one pass. I'd recomend that it be done in several passes so you can flip the neck around end for end, and that will ensure that your slot is perfectly centered. Once the slot is cut, glue in a block to butt the truss rod against , and fills in the rest of the slot.
If you use a router, it sould still be done with mutliple passes..
JasonBird