The bootmii autoboot boots by starting the original boot2 and then patches a few numbers to get the titleID from the homebrew channel in there if it needs to autoboot the homebrew channel.
I have no idea how it detects the IOS or not, but if you get the sources for "mini" which is a minimal bootmii framework, then you can check it, or "mini" doesn't even do the detection. I made a autobooter to any channel from "mini" quite a while ago, a link should be on the forum somewhere...