... a bit late to the table on this one, but it was quoted in a recent post also..
if you use iframes you should also be using the <noframe> tag to provide content for the SE's
Another way to do it is to use <div> with a scroll option and <!--#include> the xml document into the <div>.
Doesn't that solve at least some of the issue? Then in some instances using js to hide / reveal the <div> doesn't mess with the SE's cause the code is still on the page.
Dunno if I'm using way out of date ideas there, but it still seems pretty valid..