A major control which isn't mentioned - did the mothers go on elimination diets if there were allergy symptoms with their bf infants? Because that can make a difference (we know that continued exposure by an infant to his/her allergens makes them take longer to outgrow, often worsens the symptoms, and can make them "permanent") .... There are a lot of moms who only avoid obvious allergens, or who eat them anyway because they're told that they don't matter since they bf. Whereas, if infant's allergies were bad and mom switched to a hypo formula, those allergens may not have been in baby's system for months (or even a year or more) which definitely would shorten the time baby would need to outgrow the allergen, since it wouldn't be in his/her system during that time period ....
I'd have to see more of the parameters of the study in question but I'd say that it's more than likely that the study was flawed in the above respect. I know the allergen which is taking Ina the longest to outgrow, is the one we re-introduced for four months and didn't realize she was reacting to it at the time, until we did a direct intro for her at one year of age. (Eggs)
All the other evidence I've read/heard has been pro-bf for as long as possible with kids with known food allergies, and at the worst, concludes that at older ages it's a "draw" between infants ff'd with hypos and infants who were bf'd in terms of adult allergies.