He's probably correct regarding power and tunability with the new stuff. But I can't see any dollar value difference in one over the other, as long as they both work well. Especially down the road when neither the induction or the engine is anywhere near new.
Neither is stock, and modifications are a 2-edged sword in the resale market. So just do it the way you want and don't sweat the value question this early in the game. Preferences might even change in the future.
With the Ford stuff, you've got "stock" at least as far as it being within the same family. But with the FiTech it can actually appear more stock under the hood as long as you use an original air-cleaner housing.
Resale value is hit-or-miss. Nothing with regard to what you're doing is etched in stone.
While I certainly like the FiTech units (a good thing since I sell them!) I can't necessarily see just automatically changing the Ford stuff out, if it was running well and the new changes to the engine are not going to be that big. But maybe the engine builder knows something we don't about how the engine will be built.

So give us some more details please. Besides, we like to hear what people are building.
If yes to the more-power side of things, then yes to the FiTech too. I'd have to say that it's likely able to take advantage of other power adders. Where the Ford stuff "might" be (depending on what your exact setup is now), but might also be hampered by the factory tune and certain components like the MAF and throttle body sizes and designs.
Your old stuff was stock and untuned?
Long way of saying "maybe either would work" but that the advantage would seem to be in the FiTech's favor.
Let us know some more details.
Paul