A simple mitigation is to add the following statement to the atd.service 
definition:

  [Service]
  ExecStartPre=-find /var/spool/cron/atjobs/ -type f -name "=*" -not -newercc 
/run/systemd -delete

Justification:
--------------
The job command specification are files below  /var/spool/cron/atjobs/.
The naming convention is: <queue_letter><hexadecimal_epoche_start_time>

On the start of a batch job the job file is renamed to 
=<hexadecimal_epoche_start_time>.
This change the inode and „ctime“ of the file.

Assuming that '/run/systemd' :
1. is created on startup of the machine
2.  before atd is started

So we have a barrier that allows the distinction stale job files.

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