Adding status message to mail
I suppose you have tried to use drupal_get_messages() within hook_mail_alter() as well?

The reason it probably did not return a value is because the default behavior or drupal_get_messages() is to clear the message queue (so it empty the second time). You can however make it persistent by passing FALSE as a second parameter (see the documentation).

So in your hook_form_alter() use drupal_get_messages(NULL, FALSE) and then you should be able to use it again in hook_mail_alter().