This clause (and the one immediately following it) are in direct response to the "horsemeat" scandal that happened recently as well as the increasing light show on incidents of food fraud. This clause is intended primarily to combat food fraud (substituting cheap crap for the thing you thought you bought).
Prime examples include: Honey that's actually corn syrup, olive oil that's cut with other oils, dirt cheap fish passed off as expensive fish, diluting maple syrup with various inexpensive fillers, and so on.
http://foodfraud.msu.edu/Michigan State University has set up a site with information on food fraud. They also offer free online classes where you can earn a certificate and have a degree program if you feel like parting with $25-50,000.
IFT has a few articles in both Food Technology and The Journal of Food Science regarding food fraud.
The part that I'm hung up on is the following clause, 5.4.3 which says
"Where raw materials are identified as being at particular risk of adulteration or substitution appropriate assurance and/or testing processes shall be in place to reduce the risk."
So, depending on how much of a stickler you have for an auditor, having paperwork may not be enough. The issue I see is that everyone in the food chain in many of these instances has all their documentation in order. They have COA's, they have 3rd party audits, they have all of that stuff, but someone makes the choice to put horsemeat in the lasagna because it's cheaper. They dump sunflower oil into the extra virgin olive oil along with some green color because one is $4 a gallon and the other is $40 a gallon. They put corn syrup in the maple syrup because high grade maple syrup may cost over $100 a gallon while corn syrup is pennies a gallon.
I'm going to bet that they will want to see independent lab tests confirming that they items you think you are buying are the items you are ACTUALLY buying.