Yeah, the idle system is also being affected by the upgrade system, which allows it to over-scale. Just as you said, the game lacks a significant chunk of balancing.
I've read this comment a month ago and thought that I would put a lot of effort into the idle system when making a new game.
But sadly, after a month of work on Clankers, I realised that it would lower the quality of other parts, so I will be making a proper idle system next month.
Your help is greatly appreciated! :D