Yeah, just did a bit more research on all of this, and yeah, forgot about the part where BC is launching boot2...
According to this, it seems that is the way it is all booted up.
http://forum.wiibrew.org/read.php?27,8960,8977
Which means that we would have to modify boot2, not BC, in order to change the slot used for MIOS...
I would rather patch the MIOS tmd every time than do that
As for the xNEEK method, that is true, it is installed over BC, but I do not know what else xNEEK would do to actually make that compatible and function correctly. I assume that xNEEK itself would control the clock speed before launching BC?
And as for the tmd patching method, it does not store the filename as such, but it does store a value that tells which content .app no. to boot when that Title (in this case MIOS) is loaded. So, perhaps adding extra .app files form other MIOS types to one wad, and then installing, then telling the loader to patch the tmd to change which content No. is the one to boot should work.
However, I wonder what would happen if we got a loader to manually change this register here...
http://wiibrew.org/wiki/Hardware/Hollywood_Registers#HW_CLOCKS
...to set it to GC speed, and then try to launch MIOS directly, skipping everything else after setting the correct clock speed ourselves?
EDIT: @Cyan, yeah that is what I was thinking. AFAIK, it is just another slot, so we should launch it fine from other slots we install it at. We just have to try to set it to GC mode first.