That Silver dragon is the Empires emblem, as far as i know.
Not sure why its used as the "symbol" of Skyrim.
It's the symbol of Akatosh, and Alduin - the antagonist of Skyrim - is the Nord version of Akatosh.
Are people just guessing it represents Akatosh, or is there some kind of contradiction in lore?
No it does represent Akatosh. I'm trying to find the evidence, check back in a bit. For now, here is the UESP on http://www.uesp.net/wiki/Lore:Akatosh.