Marcellus,
I read it the other way. I think you've got it backwards. Time in the bunk does NOT count for absolute limit of flying hours (ie. 900 in 12 months and 100 in 28 days), but it does count for the limit on duty hours (ie. 55 hours in 1 week, 95 hours in 2 weeks..etc).
The rules all looked pretty normal until I got to that Note 3. That's just appalling.