I can see that it might be advantageous to be running under a cIOS for when launching Wiiware from emulated NAND? Presumably these need some of the cIOS features and not just AHPBROT? Could this be worked around by being able to mass change the IOS from 'IOS: Default' to 'IOS: 249', say, in a menu much like you are now able to change the default game launcher? Once this has been done then pl3 would work under 58 with all its benefits but Wiiware would still be one-click launching without having to remember to change individual settings.
EDIT: Or you could add an tag the the meta.xml for those who want to load into a specific cIOS. Or add both features...
Default for emunand channels is 249. Yes this is not so clear.... I will change it