Yes checking it twice is safer. It is usually done at FL180 on the way down. On a fleet like the 737 that is mostly domestic you become accustomed to setting it then. Then you go to a place like AUA and it is not set till FL40. Running the approach check with a second check of the altimeters helps eliminate this error. Besides like someone else said just like between the brief and t/o stuff can change. It is on the checklist twice because the pilot group had issues not having it set. If we were having problems taking off with the fmc and mcp not set properly I am glad a second check of that is included as well.