What about simply a "Browser compatibility issues" page in the themes handbook that gets linked from wherever seems logical. It would then contain things like "IE sucks so send as text/html even if your code is valid XHTML", "IE sucks and quirks mode is evil so you have to omit the XML declaration and just have the doctype", etc. (Yeah, I figure it will read like a laundry list of IE bugs, but that is the current web landscape.)
It could link to some external site for more info (there's lots of them), but it could be good to flag a few of the more common issues Drupalers run into, even if they're not Drupal-specific or Drupal-caused. People writing a Drupal theme will likely look at Drupal first, thinking it's something Drupal-weird, even if wrongly.