Ah, a walk into the swamp. My short answer (i.e., humble opinion) is that a used CSM will be worth more. They are two different markets.
There are a lot of Winchesters. A lot. That keeps the price down. Nonetheless, it will be hard to find a Winchester in original form and high condition. Yeah, they're out there, but most of what you see will have some combination of 95% finish, refinished wood/steel, after-market pads, and so forth. These guns set the base price. There is a premium to be paid for original high-condition Winchesters, but it's not that big. I'm guessing maybe 30-50%, give or take. At any rate, for a lot less than $10,000 you can buy the end-all of original Winchesters. Bought right, it's value will only go up. That's one market.
The other market is CSM. Their buyers have probably looked at the originals in the market, shrugged, and reached into their pocket for an additional $5000. What they want and get is a shooter, certifiably new and shiny, and custom made to boot. Unless I have misjudged human nature, new and shiny counts for a lot.
If you are looking at smaller gauges like the 20, the price difference between the Winchesters and CSM narrow. What I hear yo saying is that you want a custom-made shooter. Yeah, it'll cost more, but it will be what you want, and I think it will always be worth more than a look-alike original.