The factory manual calls for extra sealant. If you didn't have any, it's because some assclown didn't put any in there after removing it.
There are valid reasons to shim the midshaft.
You need to properly line up the motor with the midshaft with the pump.
The midshaft is right in the middle of this driveline tri-fecta. All three driveline components can get shimmed (most commonly just the motor).
What's so hard to understand about shimming just the bottom?

Presumably, this is done to change the angle of the midshaft driveline. Probably to align it with the pump shaft. (Though I'd rather shim the pump right).