This plugin works nicely. I just tried making an isometric dungeon by putting down an object for every wall, door, and floor in the appropriate isometric position, and it turned out great.
Is it possible to return a new seed after editing a level?
If you're asking whether you can return a new seed after putting down a few custom characters, then no, that wouldn't be possible due to the nature of how seeds work. However, you could use the "for each cell" event to iterate through the data and dump it to a JSON file, and then load the custom dungeon with the "load from JSON" action.