Jeff,
I went through the whole system with Apple a few weeks ago. When uploading to a different editing software other than P/M it did not copy images. So no Kirk, not an Aperture problem I don't believe. I'm not actually using the "Save as" command from Aperture. When in Aperture and have the images ready I simply use the "Edit with PhotoMechanic 5" command which is in the "drop down" list of commands in aperture.
I can tell you for certain that PM will never create a TIFF file because some other app copies a RAW file. PM only creates a TIFF file if you have selected an image in a contact sheet and choose the Save As command and pick TIFF as the output file format.
What does this 'Edit with Photo Mechanic 5" command do?
Let's solve this once and for all. Temporarily remove Photo Mechanic from your computer. Use the "Edit with Photo Mechanic 5" command in Aperture. Does the TIFF file get created? If so, then there is no way that PM5 created it since it doesn't exist on your computer. Put Photo Mechanic 5 back on your computer.
HTH,
-Kirk