Hey mate. Just so you know, I'm working with Unity a few days now and rule tiles system is super limited and a pain to work with indeed. Anything besides the basic tileset terrain will be a problem to make it work because require coding it to work. So I'll setup everything else and stick with Tiled for Unity too. SuperTiled2Unity importer is super easy to work with. I got it working in a few minutes and exported the sample scene to unity and everything was working fine, even animated props.
I'd recommend do the same because, Tiled is way better than Unity at 2d map editor.