I just have had a look at bricklink
http://www.bricklink.com/catalogItem.asp?P=61252
They say both parts are same mold. So you can perfectly use the official part.
But you are right with your thoughts.
The problem arises anytime TLG changes the design ID of a part. Maybe the new number should be also added to the library as an alias file. I would say yes to this as it makes things easier for the user.
http://www.bricklink.com/catalogItem.asp?P=61252
They say both parts are same mold. So you can perfectly use the official part.
But you are right with your thoughts.
The problem arises anytime TLG changes the design ID of a part. Maybe the new number should be also added to the library as an alias file. I would say yes to this as it makes things easier for the user.