Thanks for providing the dates! There has been a lot of price increases. At one point they were coming in every other week, Thursday night at midnight for a couple months very consistently.
And to your point, there indeed was a price increase between your original order date (21May) and change order date (16Jun). There was a $500 increase on June 10 2021:
Tesla Model 3, Model Y Prices Are Increasing
Mystery solved! The MBA in me can finally fall asleep tonight.
PS: the $90 extra charge is increased sales tax due to increase in order price