Yeah, I remember Bay saying something about Optimus having as much red covered up (by the flame detailing) because it is a bad colour to use in filming/lighting (when they used the actual truck prop).
As for Sideswipe not being red - I don't think it would be for preventing confusion, but more for the visual aspect of cast (promo) shots being more diverse/interesting with the colours, or any scenes with a group of Autobots in them. Kinda like how Hasbro try to have a variety of colours in an assortment of toys, swapping the release of figures or the colours of a figure to make the shelves look more interesting with different figures/colours. It'd all be marketting in the end, and how they can get the best predicted return from the options at hand.