You’ll have to be redirected to Twitch’s auth page and redirected back to your app at least once to grant your app the token. With the implicit code flow you’ll have to do this each time the token expires. If you use the Authorization Code Flow you’ll get a refresh token, which you can use to refresh tokens when they expire.
So what you could do is go through the auth process once using the authorization code flow, and then the batch file you plan to use would need to refresh the token if it’s expired before trying to create a marker but this can be done without needing user interaction as you would have already connected the app to your account.