Madame: I agree with you about the Mars Bars comparison, though I think the author might say the 'extra' calories taken in by a formula fed baby are not necessary either. However, as I pointed out, some of the extra is needed because of the extrta metabolic effort required wih formula.
You ask: I also would genuinely like to know how they work out the differences between the calories in breastmilk and formula.
They take samples of breastmilk and then average them out....overall, this is accurate enough for a comparison but you are right that at any individual feed, you won't be able to measure the calorie content of breastmilk as it will differ from baby to baby according to their needs on that particular occasion. The volume of 2 samples of breastmilk might be identical - eg 100 ml - but each sample might have different amounts of fat in it.
The evidence about obesity is growing, and there are many papers which appear to confirm the link. I think we are going to need more long-term studies before we can be sure. One recent paper indicated that formula feeding babies tend to start solids earlier than breastfeds, and it might be this that brings about the link with obesity, rather than the milk itself. If formula feeding mothers could be supported to keep their babies on milk only for longer (goes the theory) then the link with obesity might appear less.
You also say: I am sure that decreased activity and increased availability of junk food have a far bigger impact on levels of obesity.
Again, you may be right and it's hard to separate these factors out from the way these children were fed as infants. There are studies which take into account lifestyle and diet factors, but it has to be a very difficult thing to do. The obesity thing only starts to show up in childhood and later, so comparing babies and toddlers is not helpful.
There's a good paper which takes a sober look at it all \link{http://www.ibfan.org/english/news/bbriefs/bbrief38.html\here.
I like the way this paper regards it as a public health issue - this is something for society/government/the health services to take on board, not individual mothers to feel bad or scared about. The US public health machinery have declared the only cost-effective measures that are likely to work with regard to obesity are a reduction in TV watching and more breastfeeding. They regard campaigning to put both those into practice for children (adults being a lost cause, presumably) are practical and affordable.