No doubt that is true. But I don't think external programs will ever become the mainstream of modding as they won't have the same distribution support as regular mods, which will be distributed through the Steam workshop or PDX own mod repository. I see no harm in making it possible for those who really want it though.
FWIW, if you went slightly further and had some flags for only writing pieces of the save file instead of the whole thing, you'd literally have what I originally asked for.
I doubt anyone is going to make a major mod that requires external programs, but it would make *developing* mods and scenarios a lot easier. (Because conceptually that's what is happening: the AI is looking at your game situation, seeing that you need the mod to do something here, and then providing it for you.)
I mostly make mods when my friends and I want to try something weird in a multi-player game but can't find an existing option.
It's conceptually pretty easy to say "I want to change the game to explore X" but actually making all of those changes by hand can be tedious and error-prone. And there's also a limit to what you can change for a throw-away thing you slapped together in an hour or so. (Especially if you are new at it.)
That's why I'd like some tool that makes this easier/better/faster. I've thought about trying to make a bunch of structural regular expressions (for vis) that you could string together to automate changing the game scripts, but it seems daunting and impractical.
So I'd like to try using newer AI techniques. But I can't build a full AI library in the scripting code. I can't use an existing library to auto-generate content without already having a model for the entire game either. And even if I could, doing it dynamically means I don't need advanced notice and lots of forethought.
Ideally, it would work so well that it wasn't just producing one-offs, but things worth uploading as normal mods or scenarios; and that the devs of the major mods could use to create content during development.
Caveat: In theory, anything the AI comes up with could be turned into game script for a normal mod; but some things might require more entries than the game can handle, or the scripts might be too complicated for the game to run efficiently.
In other situations, this doesn't usually crop up in practice, but if there was something cool that required a companion program, we'd have a pretty solid idea of how to change the script language to fix it.