in drill, old drill operation - you can set it in cycle setting -rtrct to - auto, manual, etc.
and it outputs G98/99.
But in case of G99 (manual) tools stay in clearence plane - you have to output Z retract motion.
In holemaking it is automatic.
When you set transition/rapid - non cutting moves - direct between features - G99
if you set it to clearence plane - G98
It works for me this way.
Non-Cutting moves - Transfer/Rapid - Between Features Direct or Clearance