Just tried making my first custom system since the advanced options were implemented. The first planet I made, an Earth template, seemingly works as intended. I placed objects from various templates on it such as volcanoes. No problems. Then I made another planet, a Tropical template, and placed some metal planet objects and ice planet objects on it. After saving and exiting the editor, these all disappeared. So, it seems there's a bug that prevents objects from some templates from being placed on certain planet templates. Also while I'm at it, there really should be a more obvious way to place and remove metal spots/starting locations than arbitrary hotkeys that are not documented anywhere inside the editor.
No, that's not it. I have successfully customized several of the planets, including the Tropical one. Only the non-native CSG objects disappeared from it. It's a shame though, I spent quite a bit of time making it. This is unfortunately typical of this system editor. It's been riddled with bugs that ruin your work ever since launch, and this is not my first thread complaining about it. But it very gradually gets better so I'm hoping that if we keep posting the issues we find it might become serviceable in the future.