It's a reflection of the fact people aren't going to throw out existing filesystems because they aren't in a specific character encoding. There's nothing the OS can do about that, there's nothing programmers in general can do about that, and the only way to fix it is with a time machine and enough persuasion to force everyone to implement Unicode and UTF-8 to the exclusion of any other character encoding schemes.
And it would still be wrong, because the rules of what constitutes valid unicode have changed (what's a surrogate?), and also why would that be a good idea to bake into your filesystem??
It would be a very good idea to acknowledge the existence of codecs by storing the identifier of the chosen codec but forcing a specific one doesn't appear to be that useful.
