The go to illusion when we think of illusions is the mirage, you can see as water complete with the wavy nature of water and if you had no way of getting closer to inspect it, it might as well be the real thing. Depending on your philosophical take either it is always an illusion, or it becomes an illusion when you find out that it is not water.
A note of agreement with what seems like your main query, we might as well drop the word illusion when it comes to the physical description of the universe. Any framework of description is full of illusions that may never be proven otherwise.
I took QFT some years back and it also went over my head. There is still that mental gap of where the only way you can think about time is via time-(in)dependent wave function.