Maybe if you assume that kobo doesn't really believe their method of font selection will make embedded fonts impossible, then you could say it is a bug.
No doubt it's a "way of working" that should be changed as it trades in one problem for another.
I wonder if the new sony prs t1, with user selectable fonts, will honor embedded fonts, at least optionally, AS WELL AS ANY SONY READER DOES NOW
I don't know about the nook but display of embedded fonts in the sony is pretty limited too. So, they both suck, as far as this.