yeah 'header magic' is bad, it can give an indication, but the reality is you need a better way of specifying it to be sure.
with the MESS software lists, I guess it can be specified in the game list XML, and that will translate to some setting in the code (as would be the case with any other header)
Of course if you want to keep the open-ended approach too then supporting an open format which includes such details will be needed as well, but as you've already seen, getting any kind of traction with new ideas is difficult.
This is why I prefer the MESS 'fixed list' (be it internal or external) approach. It's just essentially a database of what each game needs, it means you don't have to mess around with the roms, or rom formats. The database tells the emulator what to do, the roms are in their native format.
Yes, some people might not like having set names, but creating even more rom formats is probably just going to result in only a handful of people caring, and plenty of people confused as to why a new format is needed, and simply ignoring it.