If the savings account is subject to automatic transfers or otherwise able to be used to make third-party payments, it may be included within that exemption. For example, an MMDA is likely to qualify. Regular business savings account may not qualify if ACH debits aren't accepted for the account and bill payments aren't permitted from it.
As for cash payments to a loan account, they are never covered by the "Phase II" exemption for non-listed businesses. The exemption only covers cash transactions (deposit and withdrawals) in their qualified deposit accounts. You didn't ask, but a cash-to-cash exchange (such as a cash payment for a change order) is not exempted, and must be reported if non-exempt transactions meet the reporting amount threshold.