Very often in halacha poskim will come to a crossroad of opinions without any clear direction of how to conclude the Halacha and the solution is to see what people are doing and establish Halacha accordingly. As well, often there is a particular “minhag” which the poskim try to understand how it developed despite being halchically questionable. When a large community of people is doing something questionable the first option is to be melamed zechut and see if there is any way to justify the minhag within Halacha (even though the posek might not agree to it lechatehila).
In the case at hand there really is only one nafka mina; whether or not these people are considered Jewish. If a posek learned the sugya and came out clear a certain way with no room for an alternative understanding, I understand why he is posek that way. If it isn’t clear, or there are multiple psakim of equal weight, I would imagine in this case they would be mekel. Although, I am not a posek…