There are certain message formats which should not be tampered. PGP/MIME attachments (RFC 2015 / RFC 3156) for example, though many mime application attachments generally don't take well to being arbitrarily modified.
Yeah. Try looking at an email before it goes into Microsoft Exchange via SMTP, then compare it to the same email that Exchange then goes on to expose via IMAP. They bare no resemblance.
Doesn't mean it doesn't happen. But it shouldn't.