Hi,
I've not really used RPG maker for any period of time, but I'll try to answer your questions -
1. You set up collisions on sprites (i.e. tiles), and the system will generate an optimized collider for you. You can make the player walk left right up and down - simply spin the Unity character controller so its pointing into the screen, and switch gravity in the sample code to point into the screen and you're more or less sorted.
2. You have layers. You can set up distances between layers, and you are free to position your character wherever in 3d space. So separate the layers by 10 units, and place your character at 5, and your character will be in behind the frontmost layer but in front of the background one. Again, you have a lot of flexibility with this.
3. You will need a plane collider for the base - even if its invisible, and then it should work with most AI/Pathfinding scripts. You might run into issues where the world is on the XY plane, and some scripts might assume that everything is on the XZ plane instead, but you can work around that.
You can paint tilemaps like from the screenshots I've seen in RPG maker, and the stuff I've described above will work, and I can give you a hand if you get stuck - just post on the forums.