The W3C is not infallible, but as Connorhd pointed out, your example stinks. The IFRAME should be taken out back and put out of its misery. And just because the W3C decided to cave and allow it to validate does not mean developers should actually use it. So to answer your question: No, it's not funny.
You're probably right about most people not knowing how to cmd-click a link to open it in a new window. So what? The link opens in the same window, as it should. If they want to look at two windows simultaneously, they can take a few moments to learn how. I think it's silly to suggest we should baby this subset of users by spawning new windows; why should everyone else have to suffer?
It's not the W3C which gives the way : but the user.
This is indeed about the user. And, thankfully, the W3C is one of the few organizations that actually puts users first, which is more than I can say for many self-serving site developers.
But that's just my opinion. I could be wrong. And on that note... have a great weekend!