I’m still not having a definitive answer from the Portuguese CAA but I decided to take this to another level and I sent an email to every EASA/JAA members.
Besides Switzerland, UK and Greece I can add the Czech Republic, Romania, Estonia, Norway, Sweden and Luxembourg to the list of countries that allow ME IR revalidation on the FNPTII simulator. I'm still waiting from other countries answers but I guess the only country that doesn't allow this, is my country... lol
You can see on this part of the JAR FCL where it states that WE CAN DO IT on the simulator.