Some interesting info about mixing "The Fly" from the Wikipedia article:
I wonder if there are other instances of this practice throughout the album, which might explain why certain elements couldn't be separated for the Atmos mix? It still doesn't explain the weird lack of low-end and overall punch.Towards the end of the sessions, U2 were unhappy with the mix of "The Fly", which was selected well in advance of the album's release to be the first single. The band ended up taking the song's mix, placing it on a two-inch multi-track tape, and adding additional vocals and guitars. The Edge and producer Daniel Lanois mixed on top of the previous mix live in the studio, an unusual practice. The Edge says the technique would "make studio professionals laugh" and believes "part of the reason why [the song] sounds so dynamic is because it was a real hands-on performance mix." The guitar sounds in the opening were created by mixing additional guitar on top of the existing guitar, creating a "really crazy natural phasing effect".