Sure you can. Under IISMgr, clicking on Binding under the site where application is created under and re-binding to domain signed cert then IISReset.
Binding info is not stored under vCAC application configuration. Those node are for cert mismatch suppression (example: cert issued to host abc.com and client trying to connect to server via IP address or alias name.) and cert mismatch suppression is different from trust not not trust (self-signed versus domain signed cert.)