Is the person working on the boat an actual up to date Mercruiser dealer? Do you by chance happen to know if they are using Mercruiser's CDS computer software scan tool or an aftermarket scan tool device such as rinda technologies for example? Also is it the same tech that was able to read your ECM when he found and cleared your other two faults such as the IAC and Shift Interrupt Switch? I asked because he didn't seem to have an issue then with being compatible.
If he's a Merc dealer and using CDS then it's more possible there could be a compatible problem as he's most likely inputting in the engine serial number and if say for example the serial number is for a 350 MPI but the internal ECM info is for a 5.0 MPI then yes I could see it coming up as not compatible.
Aftermarket scan tools I don't believe have that ability to know exactly what engine model it's truly connected to as the scan tool should only be able to read what the preprogramed info within the ECM says even if mounted on the wrong engine.
Usually "communication" problems are more common between the scan tool and ECM due to power related issues or an RFI radio interference signal interferes with the communication such as the scan tool cable is to close/laying across the spark plug wires.
So if he's a new service tech to you or not using the same scan tool that was used earlier, then it could also be incorrect software or cable cord connection issues "possibly" connecting to wrong data port wiring harness connector.
Below is an example of some information that you/one should be able read found on an ECM/PCM to know if it's the correct ECM. It's doubtful that the wrong ECM came from Mercruiser but being a 2004 engine model, the ECM may have been changed over at any time since it seems you bought this engine from someone as a turn key read to go engine?