For what it's worth : there's a world of expenses that just don't get thought about in these discussions. I've seen labor and the cost of food listed so far.
But, for each restaurant, there's also the facilities charge (similar to rent), perhaps a share of property taxes (not sure how Disney does their accounting), permits, licenses, probably a portion of the costs of running WDW-DINE is charged back to each participating location, electricity, telecommunications etc.. not to mention the stuff like silverware, plates, glasses etc that need replacing on a regular basis, the constant updating and replacing of specialized cookware and cooking appliances/tools and of course - employee benefits - which for Disney are NOT cheap.... and to top it all off.. Disney probably charges the costs of accounting for all that to each restaurant too!
Of course, if Disney does accounting for the parks ANYTHING like they do motion pictures, I can guarantee that they can show you that the parks and resorts in Florida haven't made a dime since 1971!
Knox

ain't that the truth!
to address your other points, they are accounted for in there.
Here is a
very (and I can't stress the
very enough) basic breakdown of a food service operation
total revenue = 100%
of that,
25% food cost (everything that restaurant buys as food, from spices to garnish to the actual food)
25% labor (everything to do with labor - not only wages but also benefits, incentives, training etc. from kitchen staff to cleaning crew)
25% overhead (the obvious like rent, utilities, and equipment, but also credit card processing fees, advertising, licensing, etc...if it isn't something else, it is overhead)
25% profit
Each establishment is going to have slightly different %'s, but that is a very basic breakdown. a steak house has a lower profit %, a turkey leg cart has much higher. I would guess it is pretty accurate for the whole of all disney dining together.
The executive chef and restaurant managers are running these #'s at least once a week, some daily. Monthly, they are doing a full inventory of every.single.item. in the place and getting accurate %'s. (Ironically, you work your life to be an exec chef, and when you get there you do very little cooking - it is mostly paperwork) You want to stay in whatever % it has been deemed is appropriate - you don't want to be too high or too low.
There are specialized computer programs to do this - so that they can see immediately that something is out of whack...for an example lets say food cost is running high. He looks and sees that the tenderloin cost contributed to this - why? Is the purveyor charging more? Is a prep cook cutting each steak an ounce too big, getting less yield? Is someone on the line cooking them improperly, causing them to get sent back and have to be redone?
Point is, they see problems very quickly and react. There is no way disney was losing money on the old plan, they would have seen it and reacted, not left it virtually intact for years...in some cases they did see an issue and it was corrected (see the post about the "glass slipper" dessert being taken off the menu)
Problem is, eventually revenue wasn't increasing at a brisk shareholder approved rate, so they started tweaking...hear the recent Le cellier podcast? Servings got smaller - someone noticed "hey, if I take one tomato and one mozz. off each stack, not only do i save 5 cents off each plate food cost (may not seem like a lot, but multiply by the hundreds they put out a week) but people can't share and now they order a second app. Got a nice bump from that. No one even noticed! Lets take off one more tomato slice..and so on and so on. But what happens when you have done all the tweaking, people are starting to complain, but the bosses want to see revenue keep rising? Time for a plan overhaul.
And as I have previously predicted, I have no doubt there will be another one in 3 years or so...because after the initial revenue gain, and the second year tweaking, 3rd year leveling off, they have to rinse and repeat.