You are right. The only thing that is configurable via WATO are the temperature levels (if any) from the S.M.A.R.T. check. The rest is hard coded (both the “interesting” variables and their WARN/CRIT levels).
If you want to change this, you will need to copy the check plugin from ~/share/check_mk/checks/smart to ~/local/share/check_mk/checks/smart and then modify that copy.