Perhaps it's unfortunate that BCS doesn't use some kind of designation (other than the comments) to indicate that the note is damaged and that the EF40 grade should not be taken literally. I believe this is what "NET", "Apparent", Italic means when used by PMG, PCGS/LCG. Obviously the word "net grading" implies that somehow the defects have been taken into account in the assigned grade but I don't think that's how it's used by the grading companies.
I agree that it makes more sense to grade the note as Bob describes, as if the defects were absent, but perhaps it should be made more clear that the note is damaged as part of the grade itself. "Damaged, EF 40" to make sure that the note should not be counted as an EF 40 but primarily as a damaged note with some characteristics of an EF note.
For this note, even that is being way too generous in my opinion. The comments do not convey the extent of the damage at all. There is major creasing throughout the damaged portion which would in itself bring the grade to VF or even Fine even if we ignore the numerous holes and tears. It's also not just one portion of the note that is damaged. There is fraying all along the top and bottom margins. There is what looks like a staple hole on the left side with accompanying rust and stains. The note also looks like it's been through the ringer a couple of times (see the smeared serial number) so I suspect that even the areas of the note without obvious damage are not what you'd expect from an EF note.
This is not meant to discredit BCS (or Bob's opinion) in any way. Just that grading will always be subjective and even among the best there will be disagreement.