If CCP Art. 17.02 requires a cash bond to be refunded to the defendant (after compliance and upon court order), wouldn't it be illegal for a clerk to accept defendant's signature applying the cash refund to pay his court costs/fines? Wouldn't the clerk have to first pay the defendant in order to comply with 17.02? Could he be given a check, then endorse it back to the clerk to pay fines? That way, there is a refund, and a separate transaction for the payment of fees/fines.

Also, doesn't a court also violate 17.02 when it applies (by court order with defendants' consent as part of a plea bargain) cash bonds on deposit to pay fines or restitution?

See Local Government Code 154.025 and/or 154.045 for alternatives. Also, I understand many counties will honor a valid assignment agreement when disbursing these funds. Certainly, the issuance with endorsement to the county you described would also work. In each instance, there should be an audit trail showing that the individual with the statutory right to receive the funds has decided to apply them in this fashion.