There are some flaws in the calorie system but they're not as bad as Richard Cartledge makes out. As JonB pointed out, there are weighting factors involved which account for some of the body's 'inefficiency' in processing food but they only work to a certain extent.
Most food, if chewed up properly before swallowing, will provide the body with the calories the manufacturers claim it will. Some foods which are particularly difficult to digest such as those which are hard (nuts) and those which come in a tough cellulose wrapper (sweetcorn) will pass almost untouched through the body if not chewed.
Further, the weighting effects fail to take due regard for dietary fibre (which is simply counted as carbohydrate 'cos that's what it looks like in a machine) so if something is high in fibre (all bran and their ilk) then the calorie count will be way off.
A kebab isn't difficult to digest and doesn't contain a great deal of dietary fibre and so, it will indeed provide you with way more calories than the body needs at any one moment in time.
As for 'eating lots of chocolates in one sitting is better for you than eating a couple every so often' that is pure arse gravy of the highest order. Firstly the calories in chocolate are pretty easily absorbed and if you have an excess in the body then they will be turned into storage (fat) but secondly, you may notice that if you have a large meal you feel fuller for longer because the rate of passage through the body is controlled so that the maximum absorption can take place. Fatty meals sit in the stomach longer because it takes the body longer to deal with them. High carb and high protein meals get processed much quicker. The body will still take in as much of the nutrition as it can and, if there is an excess, it will be stored as fat.