An Israeli-American friend of mine explained that when the BY Hashgaha first came out, they went by the book. The problem is that “the book” – Shulhan Aruch for example – does not teach what to do concerning complex industrial situations that may include tricky business owners. Following the book may not be enough. It’s not Baghdad in 1700.
He told me that they have since updated their practices, and the BY is as good as any other Hashgaha.