I think it's the neck itself John Suhr is concerned about not the fingerboards. His argument that figured maple is more prone to warping/distorting when used in the neck makes sense but given the amount of manufacturers using figured wood for necks I suspect that distortion is less common than he maybe makes out. Although I have heard some manufacturers that have for a long time made used of birdseye for the necks (notably Peavey) are now switching to plain maple with figured boards so perhaps it took a while for people to notice.
suhr is not the first to point it out - it basically comes down to the grain structure of figured woods. Any figuring is generally considered a defect and particularly with flame you have less grain running the length of the neck blank (more run out)
Now maple is a lot stiffer than mahogany anyway. so a nicely flamed maple neck is still plenty stiff enough if chosen appropriately. a flamed mahognay neck is more of a worry
I use figured neck woods, usually maple but there are a few rules i follow. firstly the figure needs to be consistent through the neck. If you have a patch of flame and a patch of straight grain in teh same piece then you know those sections have very different internal tensions and thats gonna lead to warpage.
The wood should be as close to quartersawn or flatsawn as possible with most of the grain running the whole length even if the flame means some doesnt.
I prefer to laminate the necks
I also add dual Carbon fibre reinforcement and a two way truss rod to most necks, especially if they have figured wood
so whenever i see a factory made guitar with a figured neck i have to wonder if the appropriate precautions have been put in place... i really worry when its a guitar thats not advertised as having figured wood in the necks