I'm not sure Michael Bay is smart enough to even be able to have that many layers of subtlety.
I think one of the problems is in the voice actors. First you have Skids who's voiced by Tom Kenny, the most quintessential white man on the planet, and then you have Mudflap, who's actually voiced by an African American. That raises some questions.
I don't think they're anything but an amusing look as some of the more silly stereotypes the world holds, rather than a straight up racist comment.