Well, the IRC protocol is all we have to work with. It would be impossible to implement an IRC client in a way that supports an unknown future protocol with unknown changes.
Agreed. However, it is an argument in favor of exactly the approach you favor as well, namely to be as consistent as possible, so that scripts can deal with such a new situation in a well-defined way as well (eg by using "/msg - $nick message" everywhere).
However, I think there is one last option that should be mentioned just as a possibility. There are very few such nicknames used by BNC software. I can think of "-psyBNC" and "-sBNC" only; maybe there's a handful in total. mIRC *could* treat *just* those cases as nicknames, as whitelisted exceptions. Then, assuming all those names contain "BNC", perhaps the "-B" switch (or so) could be reserved as never-to-be-added for those commands, so as to prevent that a valid combination of switches ever ends up forming one of those whitelisted exceptions.