Oh lol, don't worry about me, I made the change forever ago at this point. Keeping Homebrew as a part of the Mii Maker channel will break .elf homebrew loading, so if you have .elf homebrew you wish to load, then what you want to do is remove the file 50_hbl_installer.rpx from your SD card. This removes the Homebrew Channel from the Mii Maker channel, but you can still use a separate Homebrew Loader channel, which is what I was already doing, so this setup works great for me. Granted without that module I can't autoboot from the environment loader into the Homebrew Channel, but I can still quickstart into the Homebrew Loader from the quickstart menu on my GamePad, so really it all works out.