OK so the situation is different than OP's use, which was changing levels or progressing stages. Crops continuing to grow while hidden.
There are a few approaches you can try.
If I had to label one "proper" way, it would still be to use a separate layout. This is assuming you're talking about moving around, to another area or inside a building or something. You would keep track of the time that passed (there are, as usual, few ways to do this), or save the time you left the layout via a global variable. When you go back to the layout with your crops, you would compare the current time with the time you left to get the time that passed, and reconcile that with anything that needs to keep track of time on start of layout. Basically keep track of and just add the time that passed to anything that has a timer, or your global timer.
Or, you can simply teleport your character to another x/y location on the same layout, representing a building or a different area of the map. Then you wouldn't have to layer things on top of each other at all.
If you're talking about menus and dialogues, then you probably have issues with clicking and not solids for movement (you don't move around when there's a menu open right?). This would be solved, like I mentioned before, adding a "layer is visible" condition to your clicking events for the main layer and menu layers. For clicking crops, add a "Menu layer is not visible" condition, and for clicking menu items, add "Menu layer is visible".
Either way, collision tagging is probably not suitable for your situation.