OP, while its true that a perfectly fitting bike is the best template for the next one you buy, second best is surely a bike that doesn't fit in a way that you understand. In other words your current bike with the too long reach is an excellent basis for the choice (from stock) or design (custom) of your next bike. If you know that on the current bike you require have a stem that is 2 cm shorter than you prefer, then you automatically also know that you want a frame with a top tube just about 2 cm shorter assuming a 73 degree head tube and a -6 degree stem. So you can have some confidence in your fitter if he recommends something that is reasonably close to this.

But I will repeat again that you probably don't need custom or even the "adjusted" stock that you described. In this age of compact geometry most custom frame building addresses the ego more than the fit.