Just tell the agent you inquired the airport police sub-station and indeed it is a appropriate tamper-proof firearm case.

Key phrase being tamper-proof not to be altered by anyone drilling into it. Unless the DL agent had the appropriate firearm license and/or had legal authority (not a policy) to alter the firearm case you might have implied he/she could be violating the law by doing so.

Also, if there was a problem with the firearm or case during or after transport they may have some liability....