Hotkey to start and stop an application?
You can start and stop it from any app by creating a Service in Automator. First, open Automator, then create a Service in the next dialog. To launch an application, drag the Run Shell Script command into the workflow. In the text box that then appears, type the Unix command you normally use to launch ChunkWM. Save this file and pick a memorable name. For quitting the application, do the same thing, but with a command for quitting the application. Save this as well. 

Now go to System Preferences > Keyboard > Shortcuts > Services > Scroll to General. After finding the services you saved earlier, click the Add Shortcut button and create shortcuts for each one. (There will need to be 2 different shortcuts; using 1 shortcut requires more advanced Automator coding.)