Note that I’m definitely interested in adding an additional tool that will work with the kind of tileset you’re working with. It may be possible to do it based on automapping rules, but actually it would make a lot of sense to implement this algorithm in a dedicated tool so that it can be very fast and with preview.
The main problem I see is how you would tell Tiled about the structure of your tileset. Already with the terrain tool, this can be a tedious process because you need to tell Tiled for each tile corner what terrain it has. And your tileset has even more combinations. We may just have to rely on a certain common tileset organization.