Absolutely right. You pays your money, and you takes your choice. The fellow behind the V&T Lyon replica wants an exact replica, warts and all, and is paying some extra money for that, and he will get a somewhat poorer engine as well, since the original had some pretty squirrelly designs built in that could have been improved without effecting the looks noticeably.
Also, the type of boiler has a large impact on price. The Lyon has a flat-sided wagon top boiler, which was a pain in the butt to design to fit in the current code, and is a pain in the butt to build. The #318's boiler is straight, and when a replacement is built, the cost will be considerably lower due to that alone.
Then the types of corners that you design into the firebox affect the price. Traditionally, the backhead, throat sheet, door sheet, and flue sheet were all flanged over using dies and hammers, or McCabes, to make the corners of the firebox. This is also very expensive. If you can live with square corners, where one sheet butts against the other at a ninety-degree angle, and are then welded, the price goes down again. The Promontory engines have square corners, I believe, and they are not that noticeable. However, the corners on some engines stick out more than on others, and in some cases, it may be worth the extra expense of flanged corners, for esthetics.