-unless prototyping new designs and experimenting with new materials, (which should come at the makers' expense, and not transferred to the customer unless it's a custom order and the customer asks for and is willing to pay for the extra time required by the maker to work with new media and/or new designs) I think most makers should *figure out for themselves* a set number to work with as a shop rate, *and use that as a guide to determine their pricing*.
-there should generally be a standard shop rate as it applies to the experience level of the maker. This is where certification such as Journeyman Smith or Master Smith is so important, such as in other trades.
-the only other factor that should modify the price between makers, materials and experience level being equal, is the amount of time spent on a knife.
-to be fair to him/herself, a knife maker must factor in their costs for equipment and amortise over the lifespan of the equipment those costs, and factor them right into their shop rate. If a maker gets by on less expensive equipment, but charges the same, it's because they are spending more of their time making the knives.
-when it comes to other costs, such as promotion and advertising, these should be seen as 'the cost of doing business', separated from the shop rate, and be taken from the profit. It is useful for a businessperson to figure a rough percentage to spend per year on these things.
-all these considerations are for the maker. For buyers, it's important that there is some transparency when it comes down to what exactly you're paying for. This is where shop rates come in handy.
-unless a buyer is acquiring historically significant pieces, then if you buy direct from the maker you should not be paying more than the shop rate, and the shop rate should have a top out from the maker. For the maker to inflate their shop rate simply because they are popular is a recipe for disaster.
-the added expense of highly finished handmade products can only be justified by the time involved in making them. Time=money, or something.
One thing that I've noticed in researching custom knife dealers on the internets, is an often very large discrepancy in their pricing, from dealer to dealer for virtually identical knives from the same maker. Dealers have the responsibility to have a set margin that is justified simply by the cost of doing business, not their time in running their operation. This margin should not vary too much from dealer to dealer. If they cannot make a profit then it means they're spending too much money, or they need to diversify their inventory, or they need to target their advertising better or they need to provide better customer service.
...and, that's my two cents

*which I hope could be of use to a new knifemaker starting their own business*