If you add up the cost of the Pro parts, tax and labor and add that to the MSRP for the TEP (-KDSS) it's a wash. You can most likely get the TEP for less than MSRP up front which does add a bit of savings, but if you sell a TEP w/ pro parts 1,2,3 years later it most likely will not bring the same price as an actual TRD Pro, so once again you are at a wash (except for the moonroof and KDSS if those are important, at which point you should get the TEP/TRD Off Road Premium w/ those options).
This is all based on looking at internet prices, local prices, parts cost, labor cost, taxes, new 4runner MSRP, used 4runner selling prices, etc.
I did all this math for a TEP I was looking at, selling for $2k less that MSRP and I came up with an upfront savings of approximately $1k plus I got a sunroof I could care less about. Looking at vehicles for sale online on this site, other forums, ebay, carguru's, cars.com, craiglist, etc I came to realize that modded TEP's sold for close to what non-modded TEP's sold for, as mod's don't necessarily increase resale prices (this happens in the motorcycle world all the time). Where as TRD Pro's have had asking/selling prices above their original MSRP for the last 2 years.
Best advice I've seen for people who are going into this counting each dollar is, if you don't plan on doing any of your own mods, don't have access to tools and garage to do your own mods or want one of the special colors, then buy a TRD Pro. You aren't going to lose any $$, that's for sure.
If on the other hand you want to do your own mod's (especially those that are above and beyond what the Pro offers), have access to tools and garage so you don't have to pay labor cost, like the colors that the TEP/TRD Off Road Premium come in, have all the time available to do said mod's and don't mind selling w/o getting the return on investment for your mods (if and when you sell), then buy the TEP (or whatever version you like).
I think what people forget sometimes is people buy based off of what they want, not what makes sense on paper (unless what makes sense on paper is what you want, which goes back to my point of, people buy what they want!)
I think this is what you were implying OP, that the cost is not that different and people should just buy what they want. :amen: