To be honest, I'm not sure. I haven't done too much 2D in Godot, I've mostly been testing 3D stuff. However, I did a quick search and found something that looks promising.
https://www.reddit.com/r/godot/comments/6vg5v8/using_tilemaps_for_more_advanced_objects/
Basically, you would create fake dummy tiles for your interactive objects and add them when you draw your tilemap. Then on load you iterating through the tiles and and on the ones with the dummy tiles you can swap in for enemies or power-ups or whatever.