That is an absolutely terrible idea. It overrides alert() but doesn't - and can't - duplicate its blocking behavior.
I'm not criticizing you for liking the idea! I can see its appeal myself. I'm criticizing Wow Alert for letting a nifty idea result in bad sofware design.
https://github.com/al0p/wow-alert/blob/b3224bc34fea6a49aac2d...
Their version of window.alert() returns immediately after setting up the alert window and actions - because that's all it is capable of.
If you just drop this into existing code without inspecting each and every alert() call to make sure it doesn't rely on the blocking - both in your own code and every library you use - you will definitely break things.
Far better to leave alert() alone and make this a separate function with its own name.