Fyi, there have been discussions and CHtml extensions to support HTML5 in Yii 1.1, but I’m not sure what the status is/will be for Yii 2 (XHTML4 vs. HTML5 ?)
Anyway, for your last idea, I believe header, footer, and aside tags are nothing but wrappers. I personally already use them in plain HTML (not generating them by Yii).