vendor lockin is not a standards problem
"Firstly, users of the iPhone (and possibly other embedded devices) have no way of installing an alternative codec"
If you choose to purchase a proprietary device limited to certain limited proprietary software then that is your mistake and yours alone. Don't punish the rest of us for your poor decision.
"so all video sites end up having to encode things twice"
That is the nature of giving your users a choice. Mandatory elimination of such choice is no different than forcing clothing vendors to carry only one brand of clothing or forcing only one means of licensing upon software or forcing consumers to purchase only one brand of automobile or forcing all software vendors to adopt the same single licensing scheme. Choice is a good thing.
"with no guarantees that a particular format will work everywhere"
There has never been the expectation of such a guarantee before. The only difference now are the cost interests of the web services industry. The only group that benefits from the elimination of choice are those who bear competition derived costs in a diverse market. Competition and choice is always good for the consumer even though there are business costs associated with such.
"and secondly the terms of the license prevent anything that is GPLv3 licensed from working with h.264 video due to the patent restrictions"
That is all the more reason to prevent elimination of codec choice.
"This means that it's quite important that an open codec becomes the de facto standard"
If the standard is specified in HTML5 then it is not de facto, and that defeats the entirety of your point.