Why do we have SimData AND tuning XML for things like buffs?

SimData's are for displaying on/communicating with the UI. If you don't add your changes from the tuning to your SimData (that are listed) then the game will ignore anything you did change. As you've noticed from the SimData though, this is only for names, images, and a few other minor things related to the file type. So if you change the mood in the buff tuning but not the SimData, it will stay as whatever it was previously. Buffs, traits, and quite a few other files always come with a SimData, even if your tuning changes doesn't need added to the SimData or isn't visible to players. It's important to keep them together for custom mods, not having a SimData (or especially an incorrect one) in most cases can cause LUIE's and other glitches. If you are overriding something from EA and your changes are not needed in the SimData, you can generally delete the SimData as the original still exists in the game for it to read.