I think the ECU and CE, Control Electronics, are two separate things.
The CE is part of the Power Unit and comprises all the logic and control for the ERS including Control units for the MGU-K and MGU-H, DC-DC converters and between the connections between the components. It’s this that is limited to two instances in the season.
The ECU is the Standard McLaren unit which performs signal integration, control and data logging. I can’t find any restriction on the number of instances that may be used.
Fortune favours the prepared; she has no favourites and takes no sides.
Truth is confirmed by inspection and delay; falsehood by haste and uncertainty : Tacitus