Ah yes... the ballsack headstock... Not quite a strat, but in the mid-late 90s, the custom shop thought people might buy it after Fender "Cease and Desisted" them... Ah... no... don't dig it...
I believe that is a legit Charvel Custom Shop guitar from sometime around 2006-2008 after Fender took over, but it could even be later. That looks like an early "resumption of production" neck plate, before they started doing the 3D ones like the original '80s serialized production guitars.
I've seen some weird stuff come out of the new Custom Shop since Fender took over, so I'm not surprised by the ballsack, the scalloping or the finished neck. They would do whatever someone ordered really back then if you worked with them. Logos look like modern custom shop. Not that they couldn't or haven't been copied. The large headstock logo - I've seen stuff like that on new Charvels.
They make one-offs sometimes for NAMM, etc, that are nothing like what you would expect from Charvel (based on the '80s guitars anyway), so it could be just one of those oddities, or it could be a custom order. I bet it is just a custom shop one-off though - no one would order that headstock from the 90s... I don't know of anyone who makes necks with that headstock - not that someone couldn't get a one-off, but I doubt it... I don't think its a fake...
Looks like a quality guitar with some super nice looking neck wood. I vote that it is an odd, but legit, one-off Custom Shop Charvel from the early post-Fender period...
Steve