Hello Steve!
Thank you for your feedback. Somehow I still do not fully understand how the filtering with -F works.
Regarding your questions: commands executed by root user, including subshells, subcmds from script are fine for me.
I altered my audit.rules as you suggested to the following, no other rules:
auditctl -l:
-a always,exit -F arch=x86_64 -S execve -F auid>=500 -F auid!=-1 -F uid=0
-a always,exit -F arch=i386 -S execve -F auid>=500 -F auid!=-1 -F uid=0
I get entries from crond like the following in audit.log:
type=USER_ACCT msg=audit(1447855321.729:306): user pid=25780 uid=0 auid=4294967295 ses=4294967295 subj=system_u:system_r:crond_t:s0-s0:c0.c1023 msg='op=PAM:accounting acct="root" exe="/usr/sbin/crond" hostname=? addr=? terminal=cron res=success'
type=CRED_ACQ msg=audit(1447855321.731:307): user pid=25780 uid=0 auid=4294967295 ses=4294967295 subj=system_u:system_r:crond_t:s0-s0:c0.c1023 msg='op=PAM:setcred acct="root" exe="/usr/sbin/crond" hostname=? addr=? terminal=cron res=success'
type=USER_START msg=audit(1447855321.731:308): user pid=25780 uid=0 auid=4294967295 ses=4294967295 subj=system_u:system_r:crond_t:s0-s0:c0.c1023 msg='op=PAM:session_open acct="root" exe="/usr/sbin/crond" hostname=? addr=? terminal=cron res=success'
type=CRED_DISP msg=audit(1447855321.739:309): user pid=25780 uid=0 auid=4294967295 ses=4294967295 subj=system_u:system_r:crond_t:s0-s0:c0.c1023 msg='op=PAM:setcred acct="root" exe="/usr/sbin/crond" hostname=? addr=? terminal=cron res=success'
type=USER_END msg=audit(1447855321.739:310): user pid=25780 uid=0 auid=4294967295 ses=4294967295 subj=system_u:system_r:crond_t:s0-s0:c0.c1023 msg='op=PAM:session_close acct="root" exe="/usr/sbin/crond" hostname=? addr=? terminal=cron res=success'
What I do not get now are commands executed as root user from ptsX/ttyX.