The problem I have right now is the last Automaton Fishing Expansion I fixed is switching rod when under the durability, so I had a couple rods on my hotbar and the feature is using all of them.
You have AutomatonManager.AddFeature but you don't have a RemoveFeature. So I would have to rename the Fishing feature I use or maybe you could update your ToolPreservation feature... Add an option "Equip new item" under "Unequip below this level", so when the fishing rod is unequipped, you find a new one and equip it at the same slot.
Why would we need to remove a feature if we can just disable one we don't need? To override existed one? But there would be possible problem with order of the code executions. So to be safer, it would be better to have different names for features.
Also for ToolPreservation feture, you can disable it completely or partially if its functional is hinder your actions.
"Equip new item" option is possible, but for proper installation it need some additional tricky settings (picking order and other stuff), so I was just too lazy to implement it

EDIT: Actually the current AutoFishing proto is FeatureAutoFish and yours is FeatureAutoFishing, so I have both. The problem is that your FeatureDroneCommander proto has the same name as the one from Feuerteufel, so anyone with it and updating Automaton will get a cleaned ModsConfig.xml
Yeah, I probably should have used different names for my new features, but its already too late to change them, sorry about that.