So I've checked quickly, and forgot that actually, most parameters you change on material, including
opacity have no immediate effect. Material needs to be "updated".
I've played with
Base entity, and did this to it's material that has to fade:
And it did changed opacity. Additionally, ensure that initial opacity is not 1.0, because if it is, then it will not include opacity uniform into shader, set it to something like 0.999, or ensure you call
update() on material if you change from 1.0 to non 1.0.