This technology would have to make it into mainstream production first - that could still be years away. However once it is done, I'm sure that major foundries will pick it up.
However how much would making 100 Natami cores on this process cost? It's probably still more than 100 FPGAs.
Who knows? But the Reg claims their aim is for it to bring the unit costs for single wafer runs (anything from a couple of hundred to a couple of thousand units depending on size of the chips and wafers) down to the same as you get for large scale runs, so presumably that'd mean prices comparable to off the shelf Intel or AMD CPU's *if* the Register hasn't massively misreported it and *if* they meet their goals... Those are of course two very big if's

And in two years time the FPGAs will be cheaper for the same features, or faster and larger for the same cost. If Natami has something performing like a >200MHz 68060 later this year already, I think we'll be okay for classic Amiga enhancements for a while :-)
Keep in mind they're looking at producing sub 65nm chips. Even at 65nm a good design could let you get to at least 2GHz+ (AMD's Phenom series for example reached at least 2.6GHz on 65nm). If this tech pans out and becomes as cheap as they are aiming for, it'll wipe the floor with FPGA's for anything where speed matters and people have the skills and time to do the designs. Though there's still the increased complexity of designing/verifying a design that can handle those speeds reliably, so whether it'd actually make a difference for projects like Natami really boils down to how good they are at chip design.
I for one would love to get a 2GHz+ m68k compatible CPU, but I'm not holding my breath quite yet

For now it's all speculation, but it'll be fun to see where it goes... If they succeed it'll be a *major* upset of the chip business, since so much of it now is centered around a dependency on this small number of multi-billion dollar fabs and a massive barrier of entry for small chip design companies. If that changes you're likely to see tons of new startups try their hand at designing everything from new CPU's to very specialized ASICs for specific purposes.