We can edit location of all files in mirc.ini, but not control.ini and channels-dir. Why not?
You
can't edit the location of
all files in mirc.ini. In fact, the only ones you can change are for locations to store and get files that aren't directly (or exclusively) controlled by mIRC. For instance, you can tell mIRC where to store downloaded files, logs, where to load (your) scripts-- because these are not "mirc only" files.
mirc.ini, control.ini and channels\ are "mirc only" files. They're files that only mIRC needs to control. You should not worry about where they are placed.
Realize that $mircdir is not for you to "mess with" or "clean up". It's meant to store application data used by the program. You don't go into your Firefox\profiles\ dir and start reorganizing all the files firefox uses there, do you?
Your files can co-exist in the $mircdir, but you're only meant to touch your files. Leave the mirc-only files alone.