You will need to create a LOCALMOD for the CONFIG EXEC file. How to create the LOCALMOD can be found here - https://docops.ca.com/ca-mainframe-vm-product-manager/1-2/en/reference/local-service
The reason for this is the CONFIG EXEC is CA Product Code and not a configuration file. Configuration files, like the VMBACKUP CONFIG file are NOT overwritten by VMDEPLOY. However, CA Product Code is synchronized with what is installed or updated on the Code Disks maintained by VMSES when VMDEPLOY is run. Any CA Product Code that does not match what is on the Code Disks when VMDEPLOY is run will be REPLACED by what is on the Code Disks.
Therefore, you will need to create a LOCALMOD for your change to the CONFIG EXEC (or any supplied CA Product Code). Creating a LOCALMOD informs VMSES that there is a customer modification to that piece of CA Product Code and it should be used. If for some reason CA supplies an PTF update to that piece of code, then the customer will be notified when VMFBLD is run that he needs to "rework" his LOCALMOD so that both the CA update and the customer's update are incorporated.
Once the LOCALMOD is created, VMDEPLOY will know to use that version of the object as the one to use and compare for changes to determine if the object needs to be replaced when VMDEPLOY is run.