I hear you, but the SA cars absolutely hold better value than a modified car. It has to do with a lot of politics, which shop performed the mods/ diy modifications, warrantied parts, etc. Not to mention a dealer will give you close to the same value of the parts "added" to the base GT to make the SS. I agree that the SS is very expensive and performance may not be as good as the price.I think few would argue that the SA products don't hold their value better than a modified car, especially when any dealer is concerned, but that's more of a back end consideration.
It's like, "Should we buy this 5 bedroom luxury home for $1.5M or buy this 4 bedroom semi-custom home for $500k." It's about how much money you're sinking into it (the value). An argument (weaker) could be made that investing in the more expensive property will yield better resale later, but cars are generally terrible capital investments and depreciate severely over the first few decades (especially when you consider insurance, maintenance and recurring costs).
The real question is whether you feel that the upgrades are worth the $140k price tag. I'd argue no. The GT500 in stock form (to me) is better and still carries the Shelby name (although Shelby purists turn their nose up at the licensed product).
From a strictly PERFORMANCE measurement of value, (which is largely where I speak from) the Super Snake is very low value. Sure, you get a lot, but it COSTS A LOT. True, you get the uniqueness and the notoriety of having something few have, but in terms of pure performance, it's a low value purchase (only because it's so expensive).