I don't think that reddit is "backfilling." I don't have time to check right now, but I suspect that PowerDeleteSuite goes through your profile to find things to delete. Your profile is limited to showing 1k entries. IIRC that's the top 1k according to whatever ranking you're using, so you could get some more comments by re-running it sorting by top, controversial, etc, but if you made a lot of comments PowerDeleteSuite just won't be able to find everything.