Engine/ECU compatibility

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So I understand the compatibility issue with ECU/Immobilizer/keychip.
I also understand that certain years are compatible with certain engines (i.e.: a '99 cannot have an '03 motor put in it)
My question is: If the ECU/Imob/key is replaced with one from a certain year, can an engine from that year be used? Or am I overlooking something else?
i.e.: could I put a 2003 ECU and a 2003 engine in a '99 Boxster and have that work?
Additionally, I understand that the 2000 and 2001 models are backwards-compatible with the 2.5L engine, so could I put a 2001 ECU in a car from '99 or earlier?