In the following thread https://forums.galciv2.com/?ForumID=274&AID=102519, I have explained how I think morale calcuation are made. And it is scary: the influence of buildings (those that give the planetary morale bonus) is reduced by the population morale penalty. This means that if the penalty is -100%, you won't have any benefit from building morale ehancers.

And it seems to have a similar effect: population morale penalty reduce the morale civ bonus to calculate the native ability.

This means that the population morale penalty is taken multiple time to determine you planet morale, and it can prevent any positive bonus to be used.