I'd love to have the input map also (maybe optionally) save to the JSON. It would be nice to get to the original brush info, at least the way I'm using it
For using the input map with your project you can just use the .tkp file, which itself is JSON with the input map stored in the input_map field, and tileset information stored in the output_map field. I know this may mean having to load two files into your game, but the alternative of having the input map stored in all exported files would be an issue as in the majority of cases it would be unused; the file-size and game-loading time for the exported file would be doubled which could cause a problem with large maps.
Regarding the animations and tags, these could also be loaded directly from the .tkp file. The intended work flow was to export the map just for the tags, animations and tileset data, and ignore the map data if it was unneeded. Let me know if I'm missing the issue here!
Looking good on the screenshot -- correct me if I'm wrong: do the indoors/outdoors happen to be swapped in it? What appear to be room shapes seem to be filled with grass.