The S/MIME Message Specification (8/29/95) does not speak to content
transfer encodings when using multipart/alternative. So, either it is
encoded, which may result in an unreadable message if an opaque
encoding (base64) is chosen, or it may result in a clear-text message
that does not correspond exactly to the signed message if no encoding
is used. If quoted printable is used for email that might not
otherwise make it through the network unscathed, the message will be
readable and will emerge at the other end of the pipe intact.
Your concern that a message might not make it through the network
"unscathed" is the same one I have about MOSS. Doesn't MOSS compute
the signature on the *encoded* data, the same data that won't make it
through unscathed?