I had the same thought about 2 months ago. I just figured it made AA personnel more comfortable.
In the last 2 months I have traveled to Asia and my return trips started on a JL flight with all my boarding passes printed through to my home base. 3 of those times I visited the AA lounge and my tickets were reprinted to AA stock. One time, I was not able to make it to an AA lounge and used the JL stock boarding passes. I had no trouble boarding my next 2 AA flights with JL stock boarding passes.
I too think it is a waste of paper reprinting and I like keeping the JL boarding passes. It makes it easier to explain why I am able to enter the AA lounge.