The engine's control mechanisms each have a required throw; i.e. they have a certain amount they have to move to, for instance, shift from neutral to forward, or to go from idle to full throttle. You are not going to change that without changing the length of the arm the cable actuates.
Given that, you need to set up the controls so the change seen at the end of the cables matches what the engine needs.
I think most of the electronic engines have that as an add-on, rather than being strictly fly-by-wire. The mechanical controls are the same as on the older engines, they're just monitored by the electronics.
[I also think I lost the original thrust of this conversation. Sorry bout that.]
Little too hung over and not enough coffee this morning.