At least in the furniture business, the lye water treatment method goes way back.
Lyewater does a couple of things, all of them good (unless you get a drop on your skin or cloths).
It brings out the tannen in the wood which darkens all of the surface, but moreso on the darker curl or burl than on the plain areas.
This makes these darker areas stand out, increasing the contrast between the stripes/swirls.
It removes all of the oil which has accumulated on the surface from your handleing it with your bare hands. This leaves a nice clean surface for the aquafortis or stains you wish to apply.
Lye water does not attack metal so any inlays can be installed before using it.
It should be neutrilized though if only to protect your skin when you touch the surfaces.
Neutrilizing can be done with vinegar.
As I only used aquafortis once, I don't have any experiance on its effect on neutrilizing aquafortis.