Masters Ex adds side-piece character lore, which is appreciated but ultimately not important. Thats as far as it goes in terms of 'canon', since thats the only official statement on it and not your reaches.
You only think its huge because you take every single thing literally (like Olivia saying that Pokemon Trainers get 'tired' in battle too, thus you try and claim they are comparable to their Pokemon), but otherwise its its own isolated story with the biggest fanfic-crossover premises for the sake of pumping out new units for people to buy. Just look at the Arc Suits.
Z-A however is an actual main-line console game, that actively follows on from official story beats in the same developed setting, and goes into more detail about actual lore such as Zygarde, the Pokemon War, Mega Evolution etc. It adds new official content too thats going to be carried on through games yet to come. No matter what you think about the story, your feelings regarding it dont matter to the status of its canon.
They are not the same.