Firstly, I don’t know the basis of the minhag. But I did see in a sefer regarding the Oberlander city of Serdahel (not Chasidic)that the gabbaim (not the Rav) would toss apples into the shul from the attic window that opened into the shul. As I said, I don’t know the reason for it.
Secondly, there are many instances where minhag contravenes apparent halacha. For example, in Oberland cities on Simchas Torah, the Kohanim during Nesiyas Kapayim at Shachris sang 3 different songs (although now-a-days most shuls don’t sing at all). This was the minhag in Pressburg as well during the times of the Chasam Sofer. Yet see Mishnah Berura on the subject (don’t have the sefer with me now).
Lastly, regarding throwing food, nobody seems to mention that food is also thrown in almost every shul when there is a chassan’s bavarfen/aufruf. In fact, my Rav once spoke about it and indicated that although there is the accepted minhag for women to throw the candies at the chassan, there is no similar minhag for men or boys to do it. Therefore he indicated that it would seem to be assur for men and boys to throw candies/food at the chassan, although many men/boys do it anyway.