Trying to put into words the sometimes very subtle difference the construction materials make on our instruments can be challenging.
My best attmept in your example is that Mahogany will generally accept more influence from the top and back woods on a Series II, meaning it will sound brighter with a Maple top and back than one with a Walnut core.
Walnut has a little more personality than Mahogany. It's a bit darker sounding, and seems to decrease the resonance of the upper and upper mid frequencies. When you put on a Maple top and back, it will be brighter sounding, but not as bright one with a Mahogany core.
Overall, I regard Walnut to have a rounder sound. Of course this advice only applies to Alembics, other builders will have differing experiences because we each have our own techniques in empolying these woods.