Few questions regarding Isometric Tlemaps

Hello in last time I made some simple tilemap engine and wanted to move from top down to isometric maps, I have a sample tileset, which I made last day to use in game. I do plan make a game and some tools for it in unity, so all assets are needed to be loaded from streamingasset folder, which in current tilemap I achieved but it use some kind of tile prefab which is Instantiate every time the new tile is created, But I thought about making a mesh from it but here is my one question if I make a a mesh it's treated like a single object so i can't move characters behind trees. Second what is the best to achieve high perfomance on large maps, I know that using object per tile isn't good thing to do but since it's my first try on making tilemap a tried it.
Also if I use Mesh it's possible to recreate them in runtime (by adding buildings/removing trees/etc) what best approach to it is?