If they just used transparent plastic for the transparent bits, it'd be fine. (Though I still find seeing a bunch of robot mode kibble inside the car to be as equally fake looking as painted windows. Give me opaque!) but these days they don't make Transformers with enough parts to separate out the transparent bits from the surrounding area, so they make it all one big piece of transparent plastic, which means mismatched colors as the painted transparent plastic doesn't quite line up with the regular plastic, as well as more transparent plastic used on hinges, pegs, grooves etc. etc.
Modern TF's just have too much cost cutting to do transparent windows well.