Routed pockets on electric guitars are easy peezy to work with. If the builder does not have experience with dovetails,mortice,spanish heel then consider some outside help.
I would keep the wood secondary in terms of importance. You want a guitar that is lively and responsive. Since the builder is not experienced maybe consider some lesser priced woods like basic cypress sets or non figured maple and a basic sitka top. Rosewood is a luxury and privilege that I don't think is worth wasting on an experiment. We won't have the stuff forever. Maybe buy a set and keep it seasoned and humidified for the future. But don't gamble with it to start.
Since he is working electrics he probably has nice stocks of maple, consider it for a neck material. Radiused fingerboards are a godsend if your playing fingerstyle folk on the first three frets. For classical it's better to have a flatter profile...Mostly for doing barre and reaches to a certain extent.
It could be advantageous to build two guitars at once...since you want nylon, if he were to use an early martin style body platform he could consequently build a stiffer box for steel strings...much more marketable to a bigger audience and work on yours in sequence with the other one. These small bodied early Martin guitars are quite rare yet underappreciated...and I've seen many of the early ones wrecked by steel strings
Since he has electric experience I would certainly have an added transducer pickup and jack added
You only live once. Plus there is nothing better than plugging nylon into a Marshall Halfstack.