To answer your question technically, it's not a big deal to add a decorative skunk stripe to the back of an existing neck, as long as you know what kind of truss rod is inside.
If the neck has a modern double-rod double-acting (DRDA) style truss rod, there shouldn't be any problem at all. You should verify it of course, but there's probably 1/4" of safe wood behind the truss rod. Rout or mill a 1/4" wide x 1/8" deep slot down the back, glue in your contrasting wood stripe, shape & smooth.
Now if the neck has a Fender-style single-rod single-acting (SRSA) truss rod, you have to be more careful. On some of them, the rod gets within 1/8" of the back surface of the neck, right around the 5th-6th fret zone. You can still rout and add the skunk stripe, but you have to be more careful.
Most Luthiers could do this for you, either adding the stripes to existing necks that you purchase, or as a simple option on necks they build for you.
If you want true skunk stripe style necks, with Fender-style truss rods installed from the back, that's harder to find. Not many Luthiers build in that construction.
Also, when you get into directly copying Fender headstocks, that brings up the whole licensing/legal issue. Only a few of the larger aftermarket neck builders like Warmoth will do them. Most small Luthiers will not.
If Warmoth offers you everything you want, except the visual look of the skunk stripe, I would go with them. Warmoth makes good necks. Then, get someone else to add the stripes. Or, add them yourself.
