Sorry I can't answer your 1st question, since I'm on a Mac and so I actually prefer H.264. (I'd agree that Quicktime just feels wrong on Windows.)
As far as the 2nd question, unfortunately ExifTool (my usual recommend-to-everybody metadata tool) can only read QT metadata, not write. I found a post somewhere that said iView could maybe synchronize this back to the file, but I'm not sure what's become of that app now. Your best bet might be AtomicParsely, or one of the Windows-based projects listed at the very bottom of this page:
http://atomicparsley.sourceforge.net/hope this helps,
-nathan vw