>Q1: why would my bees replace the original queen? She was doing fine to me
But not to them. She may be making too little pheromones.
>Q2: should I be concerned with the new queen since she is not from controlled queen rearing? I do not the quality of the drones that matted with her.
If it were me, I would have disposed of the package queen myself, if they didn't do it for me, and I would have let them raise a new queen and I HOPE she mates with all the local feral drones who are acclimatized to my area. I have not had good luck overwintering package queens.
>Q3: hive is thriving, should I just leave it alone?