Layered tilemaps are really really powerful. There's just so much more you can do with layered maps that you can't do (or at least is harder to do) with a single one. But if it's a simple project and that's all you need, then go for it. It's all a matter of whatever makes it easier and faster to work on your own project.
I don't think it's a good idea to force yourself to use one consolidated tilemap if it gives you new mechanical issues to work through. On the other hand, if it makes more sense to you that way and is easier to work with, then that makes sense too. In the end, as long as it works right the player isn't going to be able to talk a difference anyway. Just stay flexible.