If a customer sends in a loan payment that is less than 90% of the amount due, can the bank hold the funds in a suspense account until the remainder is received without applying directly to the customers loan?

We do, and it is required on Freddie Mac loans. Our "suspense account" is on the loan level so our system shows it was received and it also shows how much the borrower owes to complete the payment.

You should check both the note and state laws to see what is allowed. Sometimes states have quirky regulations.