An easy fix without changing much would be to only count idle waste in the tank towards the dirtiness, instead of all waste in turrets, chests, ect.
I mostly agree with that, but maybe still include chests towards total waste as that may take too much challenge out of managing it if you can spam chests to contain all your excess garbage. Having stocked turrets prepared for the next alien wave, or buildings that are actively processing food/waster shouldn't count against you though, as you're doing what you're supposed to be doing with those buildings.
With those changes along with the physics fixes you mentioned to keep things going where they're supposed to I think automating something becomes fun and rewarding again!