Yup. Opened a Word file in Pages, and when saving, iCloud is the default in the location drop down. So obviously, only Apple file formats are compatible with iCloud — at least for now.
I need to sync entire job folders — a packaged ID project would include fonts and image files (Pshop and AI) as well as the production file, plus reports and instructions and other documents — so It's probably more efficient to just transfer files back and forth via file sharing (or bluetooth sharing) as I've always done anyway.
Now, if Apple wants to buy Adobe and MS, and make it all iApps, that would be just da bomb!