Applying Transport Rule only if the mail is text/plain and another if it is text/html
The short answer is that Exchange transport rules are just simply not flexible enough to handle the signature needs of most organizations, as you have found. The problem with searching email content with transport rules is that they search the rendered body, not the raw body. So if you're looking to match a MIME part header, you're out of luck.
At this point, you probably need to consider a third-party signature management product. See Better Signature Management (Exchange-bound?)