Instead of three circuits with a huge range of jet and mixture inputs, you've got a 16x16 fuel table and a 16x16 ignition table.
The idle/primary/secondary circuits are all there, its just numbers on a computer instead of a screwdriver and jets.
And the auto tune helps too, but its not the only thing that is needed.
It's a little more complicated than that (injector size, injector flow, min PW, cold start, cranking fuel, o2 correction, timing tables etc.)
BUT - I agree with you, if you can tune a carb and distributor, adjust jetting, power valves, accel pump, accel pump cams, squirters, air bleeds, distributor advance springs or MSD digital timing curves you can tune an EFI system.
And as others have said these engine were designed for EFI.
Have you played with HPTuners for NGC? Been thinking of going this route with my 05.
