Thanks for the feedback on this! Yeah, the idea behind it is basically like you suggested - to give flexibility for creating maps for your game at different scales, for example a map inside a house at a larger scale than an outdoor wilderness map. That is a good idea regarding the warning to the user when creating a new map, as well as showing the size in the Map Properties, I've made a note to add those. :)
At one point I had a "tile size" filter that would filter the tiles by size but I had to remove it temporarily after making some changes to that panel - I am planning on adding that back eventually, so that should help some, too.