I see, you're talking about landfill? That is something that SE changes, which is why it's not happening without SE enabled. I could look into making a similar sort of changes, hoping that it won't conflict with anything else.
In the normal game, you can only place landfill onto water. In the sandbox, you can place water! So, you can use the water planner to place the water, and then use the landfill to place on top of that. It's not as seamless as what you had before.