Opaque will cause less system strain since 'transparent' will still attempt to apply alpha. The reason you see transparent used instead is because most web authors don't pay attention to detail (ie, just copy-pasted some embed code they found).
BTW, you are correct about it being undocumented. The best I've ever seen is a blog by a guy who claims to have talked to a Macromedia developer about it. Unfortunaetly I can't find the link.
EDIT: I think it was this one: http://www.communitymx.com/content/article.cfm?cid=e5141