Iirc Rav Moshe says that even though the small farms are problematic since they end up at larger facilities the gzeira doesn’t apply.מדאורייתא מין במינו בטל ברוב
it's beyond how several prominent kashrus poskim have presented this as an issue deoiraysa . I also don't understand how they've extended bitul issues to kol dparish and/or ruba dlesa kaman. But I'm ears...and yes, I've asked 2 of the prominent poskim who have written about this mad the answers were less than enlightening to say the least.
(And yes, I'm makpid on cy and keilim)