Can I customize the ToolStrip to include Automator scripts? I want to include special actions in Finder such as showing or not showing hidden files. 

most of the time I want to have a clean clutter free system, however there are times I need to dig into the library or other system locations. 

It would be nice to have a way to use the touch bar to create a clutter free Finder experience that can be enabled/disabled. 

Is it possible to include scripts in the Toolbar feature of Finder or any other app?
BetterTouchTool has an alpha version which supports the Touch Bar.
You can use the ‘Open Application / Script / File’ action in BTT to launch your Automator app.