Seeking advice regarding alignment of the door stop bumper.

On a couple of cars I can't seem to get these to align in the chrome housing. They hit the housing high, maybe an 1/8" before the door closes. I have messed with the door alignment a lot. The door is aligned in every other aspect but this, if I drop the door so they will fit, then the door top frame hits, and it won't latch. Really has me puzzled. I can shave off the rubber, but it would take a lot and I'd rather not. What am I missing?  

What are the purpose of these anyway since there is not supposed to be any contact?

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