I don't think it would matter if a lot of people would run them or not. I see videos that are 3 man flawless speedruns as well as solo flawless dungeon runs that would have a place on spedrun.com. And like I said previously there would be differences in the runs. I also believe that having more categories can only be a good thing because, it would potentially mean more people spedrunning the game.

Is there any harm in making a distinction between the normal speedruns and flawless versions?

The way I see it is there are/would be big enough differences between the strats in each run to warrent differing categories.