In transformers prime, do the characters actually have biological faces or are there very tiny, almost microscopic pieces that make it seem as if their faces are made of skin (the robots not the humans, for example breakdown and Optimus Prime)
You could ask the same thing about G1 and most other iterations of Transformers besides the Michael Bay movies. It's just easier to notice that their faces are "stretchy metal" when they look like physical objects instead of 2D cartoons.
It's a cartoon. Much like how the humans have unrealistic, cartoony faces and proportions, so to are the robots given unrealistic, cartoonishly flexible faces for the sake of expression and relatability.
Staaaaahp it with your logic. Though they could be freaky straight faced the whole time like in Cybertron . Though Cybertron is a great series, the faces .