Thanks!
Are you making an animated tile?
I was working on the problem you’ve mentioned in the light of animation. If I ever finish this work, there will be a switch randomization/animation, and the latter will work somewhat like you describe. However talking about Godot you don’t have to have everything on one texture, there is special AnimatedTexture resource type which works with tilesets too.
If you are going for animation, you can split your input into 4 parts and generate separate textures with a single 47-tile template. Export the first one as a Godot tile, then replace it’s texture with animated texture, created from 4 47-tile textures. It’s a bit of extra work, but it can work even now.
As for updating program, I don’t know when I will be able to get to work on it - maybe in a week, maybe in a month.