ROI is calculated from gross investment, not net profit/loss. You have to add in the operating costs that the commissary makes back as well -- another 6 billion IIRC. So the total minimum cost to keep the commissaries open in 2012 was $7.5 billion, $6 billion of which were recouperated in sales; it's not a 2 for 1 win for the servicemember.
Not only that, you're collecting tax money from about 314,000,000 citizens (157,000,000 if you want to go with the bogus 51% number) to pay for 1,430,000 AD personnel to have cheaper groceries. That's 100 people paying $10/year for every person in the military to be able to shop at a commissary, yet the report says "Value of Benefit for taxpayers," as if all taxpayers are allowed to shop there. The taxpayer not only loses $10 for taxes supporting hte commissary, but he also loses the economic benefit of servicemembers shopping at a private enterprise in his neighborhood. There is no ROI for the taxpayer whatsoever.
I'd also be weary of hanging my hat on 'savings' figures. Every store I've ever encountered claims that I will 'save' by shopping there. Savings compared to which store? Does the servicemember hypothetically seek out deals at other grocery stores, or just buy everything at full price when calculating 'savings'? Is this number based on actual food sales, or aggregate cost of consumers buying the entire inventory vs. another competitor? Is it based on the prices they would have to charge to turn a profit?
Also, if you go back to about page 18-22 in the financial report, you'll see that DECA has some issues with their accounting practices, thus further raising the question of how accurate that figure is.
And even after all that, it still doesn't answer the basic question of why servicemembers ought to be entitled to tax subsidized grocery shopping after they have already received tax subsidized BAS.