I think mapping will be the same all the time, only different options for different fuels. Same like it is with S2000 ECUs - those from R5 should also be locked.
Different will be manufacturer, in Fiesta S2000 that is Pectel-Cosworth, in R5 it will be LifeRacing. Also wiring will be cheaper - cheaper wires, connectors, etc.
I don't know about engine rebuilds in R5. In S2000 they are mostly done by M-Sport.