well when God has a problem with it you know it is wrong

Problem right there is who's god? Not everyone follows the same religion, unless of course you are forcing your god on everyone, which is wrong.

Cybertronians are naturally able to shift from one form(giant hominid robot) to a completely different form(vehicle of some type). They even have a organ that lets them do it

Humans cannot naturally do any of that no matter how they wish for it.

No, they were synthesized. Alien race called the Creators. It's canon. There was nothing natural about them at all.

But more to the point, if you could play with the toys, watch the cartoons, watch the movie, have the lunch box, sleep in the pyjamas, and collect the magazines, why can't you draw inspiration from the Transformers to find an allegorisation within it for the identity issues you might be noticing in yourself?

Um. . .there's more than one origin story for the Transformers depending on the series. One origin story says Primus who was the god of the Transformers universe created Cybertron and the Transormers. The live action movies state they were created by a different highly advanced alien race and so on.

Because at no point can I remember any Transformer having an existentialist crisis about whether they are a humanoid robot or whatever it is they transform into. And if there was a story like that then the answer was to find the balance between the humanoid form and the transformed object.

Dinobots. You've just described the Dinobots. They had an active preference for their alt forms.

Have you even watched this show?