With regard to using an alternative ecu other than what the engine was approved with.
As the distributor for the Fadec line of controllers I have been asked on many an occasion about using this controller as a substitute ecu when an engine is sent to the AMA for approval it is sent together as a complete package IE. Engine, fuel pump, and ECU it is tested and then the approval sent to the AMA safety committee for final approval.
So while it would be a stretch to say when a screw is changed this makes the engine no longer approved when an ecu is changed this does make the engine no longer approved unless the engine goes back through the approval process with the ECU which is now going to be an after market approved ECU for this engine, this would have to be done with each and every engine manufactured and if you are thinking about the home built acceptance of the this configuration this would not fall into this category as the engine is not a home built but a production engine.