I've never encountered any difference between saving a pdf from menu commands and doing the same via a script. Be careful to select the correct settings in your script step.
I can't imagine why you'd save with Get(TemporaryPath) as this saves to an invisible folder (private/var . . . ). Perhaps it's because (I think) it will get deleted when the user logs out and that's what you want. But what if the user doesn't log out (of the OS)? I would save using Get(DesktopPath) and either delete the pdf manually or write an Applescript or Automator action that deletes the pdf.
Lastly, are you certain the problem isn't at the MyFax end?
You are correct regarding the temp path and deleting the file. It is the intended action.
Pretty certain it's not MyFax's problem. If I use the Send Mail menu step and manually attach the identical pdf file, the fonts and graphics are not affected as with the script step. However, I had already planned to spend quality time with their support staff tomorrow "just in case"