I’m not sure why you claim that individual VTs cannot be enabled/disabled from the GUI. This is possible for some VT families, but not all (see the screenshots). I’m not immediately sure why some families do not have this feature, but perhaps someone else can provide an answer.
Use the edit icon beside the VT family within the scan config edit dialog (default scan configs cannot be edited).
The explanation for seeing VTs in families you think have been disabled is explained in detail here. Essentially, Greenbone scanner maintains a dependency chain between VTs, declared via script_dependencies() inside NASL files. If you enable a VT that depends on others, the scanner will auto-enable and run those dependencies even if their family is excluded.