The process of faxing a message is the same as printing it. The fax application just renders it to a file instead of to a printer output. Since Outlook custom forms don't do WYSIWYG printing, the result you're seeing isn't surprising at all.
Whether something else is possible depends on your fax software and how much effort you're willing to put in to provide a separate output for sending to fax vs. sending to mail.
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Sue Mosher, Outlook MVP
Author of Configuring Microsoft Outlook 2003
and Microsoft Outlook Programming - Jumpstart for
Administrators, Power Users, and Developers