It would be a mistake to view this study solely in terms of breakfast calorie counts. The researcher allotted macronutrients differently for each group, not just with breakfast [1] [2] but, more importantly, in the daily totals:

Control: 1,085 calories ~ 17g carbs, 51g protein, 78g fat

Test: 1,240 calories ~ 97g carbs, 93g protein, 46g fat

Since fat contains ~9 calories per gram (versus 4 for protein and carbs) and since ~3 percent of fat calories go toward energy conversion (versus 25 for protein and carbs), we should expect Control to burn their calories ~2x more efficiently than Test. So while Control ingested fewer calories than Test, over time Test kicked their butts on weight loss because when Test burned a calorie it burned lots of additional calories. [3]

[1] Test ate 610 calories for breakfast: 58g carbs, 47g protein, 22g fat

[2] Control ate 290 calories for breakfast: 7g carbs, 12g protein, ? fat

[3] I'm ignoring some other factors e.g. enzymes (such as liprotein lypase and hormone sensitive lypase which store and release stuff like fatty acids)