You're not missing anything. Freeze plug and cover do the same thing. You can use one or the other or both. Only place for the freeze plug and or cover is the extra port on the back of the pump. This port supplies the oil cooler on cars that have one.

J. M. van Swaay

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1994 E320 Wagon, 230,000 miles
1995 E320 Sedan, 106,000 miles
1994 E500 Sedan, 79,000 miles