From my knowledge all of Klonan's (or any other dev's) mods are ideas he/someone else had for the game, but were rejected because the rest of the team thought it wouldn't quite fit or wouldn't make the game more fun for everyone.
That's why he turned them into optional mods.
Not really so much, I make mods because they are my own and not subject to the rules or guidelines of the main game.
Sometimes I make an experiment to see if something is possible in the engine, and if it is and I find it interesting, I will develop that idea into a mod.
Like with transport drones, since my first experiments with total automization and construction drones, I realised that just lettings units go from A to B is easy to do, but has a bunch of problem with the gameplay. For instance little compi bots getting in the way when trying to build.
So I wanted some way to prevent them going just anywhere, which is where the idea of the road network came from. And then there were the fun programming challenges, such as determining when networks should merge or split. I put off starting the mod for a long time because I thought this logic would be a real pain and cause me a lot of pain. It turned out it wasn't so hard (but then like 1 month later someone made a network with 200,000 tiles and I had to completely rewrite it).
And things just kinda fall into place after that.
So for me, the choice to make a mod comes from an intersection of an interesting engine feature and an interesting gameplay application.
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