I have played ranked and other modes today and continued to experience issues but I might have some pointers to what is happening.

I repaired the files and at least no "auto tap or auto accept" went through since then, when I choose auto tap it still completely non sense assign the mana for the most optimal play. It wasn't great before, but it was right 80-90% of the time, now it is definitely lower.

However, I noticed one problem the "full control" toggle isn't being recognized some times. I had multiple occasions where I would toggle full control and it would still auto resolve or auto skip phases instead of one by one or simply hold priority.
Restarting the game etc, didn't solve the issue and it happened a few more times, but I couldn't see a "pattern" why this is happening