Are the value of markdowns included in the Food Waste (loss) number?

Strictly no, a loss should be seen as a loss to the business where that loss has no intrinsic value to the organisation. In the case of markdowns, they serve a purpose which is to accelerate the sale of items close to their expiry date, the value therefore is to recover some value and profit from these items rather than donating, re-purposing or throwing away. However, again there are no standards, some retailers will have the budget for markdowns sit with the buyer and not be in the control of stores, and then there are others where the store and store operations will own the budget for markdowns.