I think it's more of supply and demand.

Back 10+ years ago, I was looking for Gen3 4Runner in 5speed manual. I found one, but it was priced about 1500$ more than auto. (private seller) The seller knew it was rare, and there's a sucker for every seat, I was that sucker, ended up forking out the asking price on it, because I wanted it. In the books, manual transmission didn't change the value, if anything made it worth less. You know what they say, Kelly doesn't sell or buy cars.

I lucked into buying my Sport PKG, (with help of people here) couple of months ago... I don't think the Chevy dealer I bought the GX knew the difference between Sport PKG from Barbie Pkg. (Neither did I, before I got educated by the people here) Pricing was similar to any other GX with similar miles and other options. (Nav, etc)

You're going to run across that one person in million that wants Sport PKG, and I'm sure he'll pay handsome extra for it, as I did for manual transmission on 4Runner.