Just tested in 15.0.3.7:
- enabled the system rule;
- created a BOM with the component of qty = 3, with the flag selected;
- released an SFC and opened CT500;
- CT500 showed qty = 3 but I changed to 5 and assembled successfully.
The behavior you are describing should have been changed a while ago. At least in 15.0 this seems to have been done.