Howdy JW and welcome,
Body wood: Mahogany is more focused than Rosewood of any kind. It’s not really a substitute. IF you like the Brazilian sound, consider Indian rosewood or perhaps cocobolo.
Top wood: I found German and Italian spruce to have a bit more ‘bell’ in the top end than Adirondack (Red spruce). But has been years. So defer to more up to date opinions.
Fret markers: As long as there are marker on the side of the neck, looking up at me, I’m OK. The big ones on the fret board are for show.
IIRC, more than 50% of SCGC’s output is custom. Usually they are variations on existing models. Give the shop a call and discuss. They’ll be happy to talk to you about all this!