I have never heard of another app that deletes user preferences when doing an minor dot update. In general this is considered bad practice in my understanding. If we did this to our customers they would not be happy.
I rarely do the updates, only did because support asked I do so when working on another issue. Because of this rarity of doing updates my team and I forget about this odd preference that breaks all automation.
If they unwilling to fix the update process to not reset the preference, then I would suggest changing the default to the more usable and common state of Off. Are there really that many people testing Windows Store Applications?
