Yup, it doesn't run automatically for exactly this reason. It outputs "suggested_shortcuts.yaml" and I can copy and paste from that into "shortcuts.yaml" so I have manual control over which shortcuts are live :)
This is good I can imagine all of the embarrassing auto typing. It is the reason I hate Android phones. I will be typing and it will try to predict what I am writing. Some of it not sure what data it is built on came out hilarious or down right inappropriate. Not like swears or vulgar just the punch of the expressions.