Ah, now you hit upon a stickier subject.
What you are encountering is not a bug, however I understand your position.
The reason you do not see resources in the Factorissimo 3 surface, it is not generated with resources in the surface definition. The same issue occurs with the Subsurface mod.
The "ignore planetary restrictions" is there so you acknowledge that by placing those other resources, you are likely going against the mod's intended game play. It was not Factorisimo 3's intention to have resources placed inside. It could break actually it in some situations, I am not sure. I think you can move the factories, but I doubt the mod author expects resources and moves them too. Maybe it does? I have not tested it. :)
That said, I could have the code auto-click "Ignore planetary restrictions", if the surface is not a planet. That seems reasonable.