I think the OP's original question is a good one.
Here is the deal as I see it: New home purchase (from a merchant builder, KB Homes, for example) is the one instance where a buyer can semi-customize their home with finishes and upgrades to their taste (within whatever is being offered by the builder, for the most part) and include those modifications as part of the purchase price. It is the one scenario where we have an itemized breakdown of what that buyer and that seller agree those differences are worth. In the resale market, that dynamic doesn't exist; although we can see something similar. In many of my markets, homes are sold as the "before"; the buyer is purchasing the home with the intent of spending money to do X and Y to get to the after. Cost is certainly a consideration in their purchase decision, and the price differential they pay for a home in X condition vs. what the Y home sells for includes cost.
Depreciation is what we use to adjust for something that is new today vs. what it is worth after aging 5 years. Most appraisers apply that in the age or condition rating adjustment. In theory, if someone were overpaying for an upgrade in a new house, that would be treated as functional obsolescence. I don't see too many adjustments in the cost approach for new homes for functional obsolescence due to updates/upgrades (but certainly, if a buyer opted for the highest priced upgrade for all options, that would likely create some functional obsolescence. So while I rarely see it, it can happen).
By using a re-sale, we have additional data to include in our market value analysis of the subject. But all things being equal, the expectation would be that the newer home sells for more if for no other reason than depreciation (the resale has it... the new house probably doesn't).
Not all markets are the same, but in the markets I work within, and in regard to merchant tract development...
A typical buyer would prefer the new home vs. the resale (even a year old), all other things being equal.
A typical buyer would consider purchasing the resale vs. the new home if the price of the resale was less, all other things being equal.
The discount necessary in price of the resale vs. the new home in order to get the typical buyer to purchase it vs. the new home is depreciation (again, all things being equal).
So the expectation (in my markets) is that all things being equal, a new home will sell for more than the resale, all other things being equal. That's the new home premium; in stable and rising markets, it exists. In a declining market, it may diminish or disappear..
Assume that a "good" kitchen upgrade for a new home costs $35k (a number we get from the builder's list). This includes appliances, cabinets, and countertops. If you look at Life expectancy tables, you are going to see that (while each component has a different life expectancy), the blended life is going to be somewhere around 20-25 years. Let's split the difference and go with 23 years.
5 year old resale has the same overall quality of kitchen. What's the supportable adjustment using cost & depreciation alone? About $7.5k. If everything else is the same except for the kitchen, and assuming the the improvement has a Total Economic Life of 65 years, the 5-year old home with an effective age of 3 years has 2% depreciation. If the improvements cost $200k to build, then that is $4k in physical depreciation.
Would it be unreasonable to see a $10k to $15k difference in price between the resell home and the new home, given the above? No, it wouldn't. Would it be unreasonable to see a $50k difference? Yes, it would; A $50k difference would need more investigation. A $10k to $15k difference? No, that would be more in line with the expectation.