What you are saying about the upgrades, including to some extent the lot, is essentially true. However, how it can help is with resale. For example, I did a semi-custom build on one of the nicest lots in the subdivision where I used to live. The builder (a small, local builder) did not charge a "lot premium." When I had to unexpectedly sell less than two years later, my lot was a BIG selling point. It was significantly larger than most of the other lots in the 'hood and it backed up to a green space. The people who bought the house could have gotten something in the 'hood for less $$ (or even in another development), but they really wanted the premium lot. Same thing with upgrades - there are some that have a lot more value than others (for example, HW floors and a 3rd car garage), and a GOOD appraiser, realtor, and knowledgable buyer should take this into consideration when considering comps.
As someone who did have to resell a "semi-custom" not long after buying it, it can be a real PITA, especially if there is still new spec construction to compete with. But, if you can do something that sets your house apart from all of the others, that will certainly make your house more desireable and, depending on the upgrades, help your house at least hold its value, should you have to sell.
Here in Harris County, nicer lots do sell for a premium and the county even asseses the value of the lot based on size, so here you sort of have a case for asking more for a house on nicer lot. In Brazos County, all of the lots in my old subdivision were valued the same by the CAD. However, I was able to successfully get my appraisal modified when I purchased the house because the appraiser significantly undervalued the lot compared to what my builder paid for it. My point here is that lot value is VERY subjective, so it might be worth doing a little homework to see how it is handled in the area you are interested in.
[This message has been edited by TXTransplant (edited 4/4/2014 8:47a).]