How would Apple be shafted in this scenario? Sure, there are no On2 hardware decoding chips in the iPhone, so battery life would suffer a bit, but... is there anything more than that?
Consider Flash vs Apple. There's nothing stopping Apple implementing Flash, they just don't want to.
If Flash becomes indispensable for the mobile web Apple will be forced, eventually, to support it. But up until that point (which may never come) that it becomes inevitable, and probably for a long time after that point is reached and Apple actually caves, all that Flash content will not be accessible to users of iPhones or iPads, which reduces their value to consumers compared with Android equivalents that do support Flash.
So the same as that, but with Google codecs and web content in them in place of Flash, but worse because in this scenario Apple probably wouldn't support them on the desktop either.