After 10 days of review by Google Play team, Migrate helper has been published on Google Play.
Download link: Migrate helper - Apps on Google Play
From this version onwards, migrate helper should no longer be flagged as a harmful app.
1. This version uses 2 add-ons. One for restoring calls and sms, another for settings. The add-ons come bundled with the app.
2. The watcher app has been removed.
3. A new option has been added to remove the helper from TWRP.
Please note that this is still a very rough version, things may not work. I will continue updating the app. Please try only if you are adventurous. Feedback is always welcome.