I'm used to the PC world where battery/heat are hardly a problem and software rendering is usually a bad thing when hardware rendering is available.
The biggest cost is memory. Every pixel of hardware accelerated web content gets 4 bytes of memory. This adds up quickly, especially since any content that overlaps hardware accelerated content must become hardware accelerated as well.
The other big cost, as olsn already pointed out, is that blending these offscreen images onto the screen takes time and power on every frame. In extreme cases this can cause scrolling to stutter.
See the "Optimizing Web Content in UIWebViews and Websites on iOS" session from WWDC 2012 for more information about this.
The bottom line is, that Apple forces developers to take care of this instead of having everything automatically hardware accalerated and therefore shortening the battery life of iOS devices(by a lot I'm guessing).
Does rendering a few more polygons actually kill battery life that badly? I believe much of the OS is already hardware accelerated anyway.
No need for workarounds and hints in an application whose main function is to display _documents_.
The issue affects websites as well as hybrid apps. Given that this change is poorly documented by Apple, and it directly affects a JS plugin I'm working on, I'm quite grateful for the OP sharing their findings.
The WebKit developers spend all day trying to drive the web forward. That's what they do. They're not pulling their punches. Try hanging out in #webkit on irc for a bit and see if you think they want the web to lose to native.