To clarify:
I think this is wrong since the next line is a comment line and the script editor is not suppose indent the next line.
This is either wrong, or meant to be:
I think this is wrong since the next line is NOT a comment line and the script editor is not supposed to indent the next line.
I don't think it should indent, but it shouldn't treat the next line as a comment either. $& should have no meaning at all within a comment.
So yeah, mIRC doesn't treat the next line as a comment, it only indents wrongly because of the $&