FWIW, in my opinion it would be difficult to give such a broad generalization of a "markup" on new/ nearly new, production aluminum/ fiberglass and custom built boats. Way to many variables to consider between them. Would be like trying to compare production costs/profit margins of an Audi 8L to a Pinto without knowing what options/trim levels were selected.
I would suspect that to even to get in the "ballpark" wrt "mark up" you need to compare apples to apples. When I had mine built I compared the base hull, construction material, thicknesses, prices, design, build quality, standard options, etc., etc., of the model/s I was interested in and added similiar options to each. Was still not an easy task. What I found at the time was that the base price of the hulls of the different manufacturers that I was interested in were fairly evenly priced based on my observations. Not saying that were all the same as that would be far from it, but once I factored in build quality, similiar hull design, longevity, re-sale value, etc. I felt I was able to make a fairly informed decision. It allowed me to sharpen my pencil a bit but I wouldn't expect any huge discounts from a manufacturer of a custom built boat. From my experience there was very little room on the price of the "base hull." The upgrades were all pretty much at a fixed price across the board, (cleats are cleats and down rigger mounts are just that and, although not the same price, are similiar across all manufactures and fairly easy to compare) but the discounts did increase with the type and amount of options added and those were quite different across the board in quality and price. The electronics....and installation.. well that's something else and can add up very, very quickly and about as easy to compare as snowflakes. Engines, don't expect much if anything. In the end it will come down to condition, quality and demand of the product you or the next person that's waiting for it feels its worth. A waiting list definitely = an added premium and less of a negotiating position.
Good luck hope it works out.
