As those profiles are based around the "Wait For Spoken Response" action, which runs synchronously, meaning the command waits for that action to be complete, it's not really feasible to just add a "Wait For Joystick Button Press" or "Wait For Key Press" action to it.
Assuming you only need one input method to advance the checklist, the simplest modification might be to just strip out nearly everything, and make a few modifications to end up with this:
MODIFY PATH AND FILE BELOW FOR YOUR CHECKLIST
Set text [~textfile] to [C:\Checklists\Checklist.txt]
-------------------------------------------
Start Indefinite Loop
Set integer [~targetline] to [~targetline] plus 1
Inline C# Function: Get line, wait until execution finishes
Say, '{TXT:~lineOutput}'
Begin Text Compare : [~lineOutput] Equals 'checklist complete'
End Condition - Exit when condition met
Wait for joystick button press [Joystick 1 Button 1]
End Loop
(obviously the file path would instead point to the relevant file on your system)
Stopping the checklist before it's complete would just be a matter of stopping the command itself, E.G. using another command containing the "Stop Another Command" action, or by stopping all commands.
As an aside, while it's certainly good that users share their profiles, and I don't intend to disparage them, this particular profile/command would not be an example I'd personally recommend learning from.