Apple has made it known through its chip design (and subsequent underclocking), app development limitations, etc. that battery life is of utmost importance. I suspect that some of these limits are an attempt to keep websites from draining mobile devices of energy. Is WebGL over a browser typically as performant as native code? I would suspect no, but I'm not familiar enough with WebGL to know.
It's unlikely to be battery concerns. If anything, lack of extensions and low limits means webgl code would have to perform multiple passes of a scene to achieve the same visual effects, thereby increasing the battery drain. Also, why allow these features for native apps if it's not good for the battery?
And if you click through to the webkit bugtracker, it looks like almost all the issues listed already have patches committed.