If a teller cashes a check with three payees listed and three endorsements on the back, are all three considered beneficiaries on the CTR? If the check is properly endorsed but only one of the payees brings the check in, are they still all considered beneficiaries, with only the one who brings the check in, as the conductor?

If it were me, I would start with the assumption that the transaction is on behalf of all payees. Then if the person actually present indicates that the transaction is only on his behalf and provides a reasonable explanation, I would would accept that and treat it as though the person were acting only on his own behalf. And I would document the reasons.