I am only speculating, being a non-Warmoth-employee, but it may well be that the Snakehead CNC program is based on the Total Vintage one-piece neck program, which may differ from the two-piece neck programming.
My guess is you'd be able to get a Snakehead custom cut from a two-piece (i.e., shaft is one wood, fretboard another) for an upcharge, as others have suggested. But the small dots may well be integral to the Snakehead programming.