The only time you are likely get your money is if you are building a commission for somebody generous. Otherwise, you are building for your own enjoyment, and that is difficult to put a price on.
The point about a well made scratch built model being unique and therefore having a higher intrinsic value at the auction house is fair enough, but pity the scratch builder who makes a superb model, and then the following year, a kit or RTR of the same prototype appears on the market.
At a show a few years back, the best in show went to an Edwardian lake launch. Beautifully scratch built. There were people who refused to believe it wasn't one of the kits of the same prototype, and seemed unable to comprehend that the two models would look much alike.
And then there are the auction houses themselves. On a recent "flog it" type show a guy had an old tinplate train set. "0" gauge. The presenter "expert" pronounced it as a Hornby clockwork set, as did the auctioneer. Nobody seemed to have seen the great big makers name of "Mettoy" printed on the box in four inch letters, and appearing on every single part in the box.
However much time, effort, skill and resources you have put into your model, it is worth in money what you can get for it on the day.
A model shop has to guess what the market is like in their area. Putting a price on that is pleasant for the seller may stop it ever selling, and having a possibly large item taking up space that is being paid for might not do the shop owner any good. At the end of the chain, the person paying the money decides the price, either by agreeing with the price on the label, haggling it down, or moving on.