I don't think you get what the .ini files are doing, or what they're intended to do. LLE audio isn't a "compatible" or "incompatible" setting. I can play SMS just fine with LLE audio or HLE audio. HLE audio isn't forced by the .ini because this game works equally well with both (and this has historically been the case for years in Dolphin) therefore Dolphin leaves it up to the user to choose whichever one he or she wants.
It's not up to the .ini files to automagically know if your system can handle LLE audio and prevent you from using it. The default settings in .ini files are not meant to completely replace a user's settings, just specific ones that are thought to be the "recommended" ones. If a game can run fine with either HLE or LLE audio, neither is specified in the .ini. If one games plays noticeably better with LLE audio (Wind Waker used to be one such .ini) then LLE audio is forced through the .ini.
It's not up to the .ini files to automagically know if your system can handle LLE audio and prevent you from using it. The default settings in .ini files are not meant to completely replace a user's settings, just specific ones that are thought to be the "recommended" ones. If a game can run fine with either HLE or LLE audio, neither is specified in the .ini. If one games plays noticeably better with LLE audio (Wind Waker used to be one such .ini) then LLE audio is forced through the .ini.