Beneficial ownership rules don't worry about the ownership
of a loan, they apply to "legal entity customers." In this situation, you have two customers, one of which is a "legal entity customer" that is subject to the beneficial ownership requirements.
Said another way, don't get hung up on the "ownership" of the loan as you need to look at each customer (i.e. borrower) to determine if they are a legal entity customer. If they are, the beneficial ownership rules apply. In theory, if you had three entities as co-borrowers on a loan, each would individually be subject to the beneficial ownership requirements as each would be considered a legal entity customer.
None of the human owners of the Entity meet the 25% ownership threshold.
Just to confirm, are you saying that none of the human owners have 25% ownership of the legal entity? Or are you saying that none of the human owners have 25% ownership of the loan? Again, keep in mind that the ownership of the loan doesn't matter as we are concerned about each legal entity customer. Therefore, the ownership prong would only NOT apply if no individual had 25% or more ownership in the legal entity customer - in other words, the ownership of the loan is irrelevant.