How did Atlanta FM become a mess? There's any uniform plan for the ATL metro area. There are lots of Rimshots stations, but not much metrowide radio stations. The only radio stations that have towers near the center of Atlanta are.
Atlanta was still a relatively small town when FM was being born. Look at the central Atlanta FMs you cite, and most of them match up almost exactly to the AMs that existed in the 1940s/50s/60s: 92.9 went with 1190, 94.1 with 790, 94.9 with 1420 Decatur, 98.5 with 750, 101.5 with 1080, 103.3 with 590. 96.1 and 99.7 were independents. That's about as much radio as the Atlanta of that era could profitably support.
In the meantime, Atlanta is just close enough to other fairly sizable metros (Chattanooga, Birmingham, Augusta, etc.) that by the time the city started growing and FM started booming, a lot of channels were already spoken for in those areas or in smaller communities just far enough from Atlanta to have their own identities (Athens, Rome, even Gainesville and LaGrange back then.)
Until the 1990s, it wasn't as easy to shuffle the dial to move a frequency in - remember the first, failed attempt to bring 100.5 in from Anniston to Sandy Spring in the late 1980s?
In retrospect, north Georgia should probably have been part of the Class B spacing territory, which would have allowed for a few more signals to be shoehorned in when it would still have mattered.