It seems that CRKT discontinued the Crawford/Kasper Professional with AUS8. If you're going to go to the expense of having the knife customized, you might want to get it with a "better" steel that might be difficult to find later.
However, I know that aluminum-handled CRKT M16's have only one liner. The KFF Pro might be the same. Or maybe not, given that the KFF uses a stop pin rather than the thumbstuds.
Regarding the holes, it would be easier to do without, but I imagine that most any well-stocked shop would have the right-sized bits for the job. Since the customizer is going to have to hit the pivot, scale attachment and possibly the stop pin holes with some precision, it would probably be a trivial thing to put the holes in the handle.
Wait a minute-- holes in the handle? I thought only the Pro had decorative holes? If you're only referring to screw holes, I've found that one can cut down on the number to save time, drill bits, taps and one's sanity trying to line up blasted little holes. I would go for two or three in the liner (with at least, I suppose, 2 through the backspacer) plus the pivot for scale attachment. Alternatively, you could hide the pivot under the scale but then you might want to find a scale attachment point further up the scale for stability.