I believe the cap is just to prevent dust and dirt from finding their way into the bearing behind the seal. Here's a post about my thoughts when I first got the seals/caps
. Includes pictures of one installed on the ATX tranny. You can't tell just from looking but the axle hole is about 4mm larger on the ATX tranny (allowing the cap to be installed).
Here's the pic where you can see the silver rim around the MTX seal. That is what is making me think there should be a cap there, it's fresh silver, looks like a cap used to be there.