Definitely the lyrics. As a couple already said, submarine/gasoline comes almost immediately after "......can you see it too?" The other verses are the same structure though not even close to the same words as far as I can make out. The only thing I heard constant from the verses was the "wars between nations."
Beach clip is obviously not very good quality to know completely, but it seems like the song was mixed and arranged better. The drums and base seem more up front and Bono soars without being intrusive. The instruments do a lot more work in the song than the beach clip and both have this characteristic more than say Miracle drug or others where Bono yells over anything meaningfull from Edge or Adam.
GOYB had to be the most straightforward song in the beach clips, and even that changed, not significantly, but at least considerably. We know breathe has been through a few lives, so thats one clip that is different, UC and magnificent have probably been similarly re worked. The fact that boots sounds structurally the same cant be read into too much. All the other b clip songs sounded like there was alot more room to experiment/change things.