1) Wiring Problems - In the very first episode, the yellow one whose name escapes me falls of a cliff in car form. He is asked if he is ok, but he thinks "He sprained his gear belt". he is then asked if he can transform, he says "I think so." This indicates that certain damage can render the transformation system inoperable, thus suggest that the wiring is engineered to allow for transformation.
2) They use Energon. Energon can be any fuel source - electricty, gasoline, whatever, can become energon. So any fuel is acceptable.
3) The robots are sentient because they come from an alternate planet where Silicon based lifeforms exist and evolved. Keep in mind that silicon is directly under carbon on the periodic table - it's theoretically possible.
4) They looked very different on their home planet. In the first episode, when they are awoken, the ship's computer finds examples of machines (Which, presumably, it takes to be life forms) indigenous to the area, and reengineers the transformers to utilise those shapes.
5) Universal Translator. All languages follow some sort of structure rules, so a significantly advanced piece of software could pick up and translate it.