Hi
S'funny you should ask this - I recently took delivery of a well used 2004 Petrucci and took it around my mates guitar workshop for a "look see".
My mate is a guitar builder and his business partner does amp/keyboard repairs.
He asked why there was a definite "cut off" point on the neck behind the nut. I do excuse him for this as he is a drummer
I had to explain that this was where EB in their manufacturing process clear coat the rear of the headstock. The remainder of the neck is sealed with gun stock oil and wax making it prone to absorbing dirt/bodily fluids and as Beth says "mojo" from guitar playing.
My Albert Lee guitars being relatively new do not seem to have mellowed that much but looking at photos taken when the guitars were brand new, quite clearly there is a darkening.
On my EVH and Pet the colour has darkened considerably - not dirt just (as they say in the antiques trade) a patina. I guess you could actually call it antiquing!
Hope this answers your question - if not come on back.
Spud