Back from the dealership, they cleared my second CEL.
The guy there did receive news from Toyota France: according to them, the ECM re flash *does not* solve the problem and is only there to temporize and give them time, because they say they need to replace some parts in the engine to really fix the problem. This is the opposite of what Toyota says in other countries...
Bear in mind that the same guy is also telling me that there is NO problem at all with the fuel pump (engine chirp) even in front of another GT86 that does the same noise. His argument is that you can't look at what is going on in the other countries because "they are not the same parts and not the same cars". I can understand that there are differences in the ECM software due to local legislation, but come on... Anyway, I don't know who to believe anymore.
My guess is that there are varying degrees of deficiencies in the engine parts. Small ones will be "fixed" by the re-flash (or that they will fail again in a few years when you are out of warranty), large ones will need to be changed with better parts.
This is starting to make me mad. Not at the car itself (every new piece of tech has issues), but at the way this situation is handled by Toyota in the different countries, and the typical dealership behavior of denying everything even with factual data in their face...