If the airframes are being manufactured using low cost manufacturing, that shouldn't be too much of an issue and as long as they are all using the same systems, or subsets of components from those systems, I don't think that should be that big of a problem. That's another reason why I said they would recommend a family of powerplants with various bypass ratios, etc, but the cores would essentially be the same. For instance, just look at the F404 and F414 and all of the different variants developed from those. So, similar to what SFerrin said, you could have a basic core F414 type, a basic core F135 type, and something off the shelf/commercial for the high bypass turbofans. In a sense, the USAF/DOD become the contractors for the systems and let the airframers have a catalog of approved systems to choose from; which I think could also help to lower costs, in the way the rapid prototypes office does, because, IMHO, the systems should already be proven.
This allows long development cycle systems to be in continuous development, separate from actual aircraft programs, in the same manner that physical PC's are separate from the OS development cycle. Also, as much of it should be "plug and play," which I know they've been working towards, as possible. I mean right now, look at all of the modifications that have to be done to airframes to upgrade radar systems. It would be nice to have a standard attachment/connection/power system, so they could be rapidly changed out based on new developments. It seems to me, this is what they are working towards.
