Remove pacct_shadow.d/ pacct_source from /run before starting and after stopping.
systemd rightfully wants absolute path:

[/lib/systemd/system/atopacct.service:9] Executable path is not absolute, ignoring: rm -rf /run/pacct_...ct_source
Expect 143 as successful exit code, cause systemd sends SIGTERM(15) and atopacctd adds 128 to it:

428         if (cleanup_and_go)
429         {
430                 syslog(LOG_NOTICE, "Terminated by signal %d\n", cleanup_and_go);
431                 return cleanup_and_go + 128;
432         }
Remove /run/pacct_shadow.d and /run/pacct_source after stopping, not after startin atopacctd