Currently PCGen can only identify ability score bonuses directly granted by equipment objects or equipment modifier objects as coming from equipment. If the bonus is delegated into an ability, is loses this association, and the skews the output of the STAT.NOEQUIP output token.
PCGen must be able to identify these delegated bonuses as coming from equipment.
Unfortunately there seems to be no programmatic way to identify how the object that granted a certain ability object to the character.
However, there is a workaround. PCGen can test if a bonus comes from an ability, and if so, if that ability has TYPE:Equipment. This is a hard-code, but for the time being it makes sense, especially considering that the STAT output token is destined to become deprecated in the long run anyway.