Hi John,
Can you please confirm the version of Adobe Reader intalled on your iPhone and iPad, beacuse flattening option is available on both iPad and iPhone in the latest version of Reader.
When you mail pdf, then you might not be able to see the comments (which are not flattened) if you are viewing it in iOS preview. If you will open the same pdf in Adobe Reader on desktop or any other pdf viewer, then comments will all be there.
Hope this helps.
-Charu