Noah Gengo this thread is talking about the new feature added in todays beta release which allows you to disable the collisions on a per tile basis in a tilemap. Which means you don't have to have a separate invisible tilemap for collisions anymore. Although that approach does allow for additional flexibility in how your collisions behave at runtime.
newt you could always have 2 copies of each tile, one with collisions disabled. I would have thought normally you'd want to change the visual aspect of a tile if it went from solid to passable. Even if you didn't this would give you the flexibility to do it later if you wanted.