Is there any way to make auto pause works during schedule workouts?

Hello, there is not. This is because the automated alerts take priority over alerts set for free run. There are a couple of reasons for this. One is that if you have a pace alert set for your easy runs of 6:00-8:00 and your workout is set for 5 minutes at 5:00-5:15 pace it can't run both alerts at one time. Another reason is the Coach workouts are designed to be run as continuous workouts, and thus you would like to avoid pausing the activity as much as possible. Obviously pause for safety purposes, but otherwise I would minimize the amount of time spent pausing your workouts.