Their whole goal with the pricing realignment is to make the "per minute" charging as close to "per kWh" as possible. This means that when charging at higher power, the price needs to be higher as well because in each minute of charging, you're getting more energy. So, for example, let's consider Case A: 3 minutes of charging at 60 kW vs Case B: 3 minutes of charging at 180 kW. For A, in those 3 minutes your car actually got 3 kWh of energy during that time period. For B, your car got 9 kWh, i.e. three times as much energy in those same 3 minutes. If the goal is to have a pricing tier strategy that as closely as possible approximates a per kWh price for the energy then the tier at 180kW needs to cost three times as much per minute for that to work.

Basically, what Tesla did is realigned their pricing tiers for locations that charge by the minute so that even though you are technically charged by the minute the end result works out to you effectively paying a price that is very close to their desired $/kWh target.

As for why they don't just always charge by the kWh, they can't. Tesla would like to do just that, but in many places they are prevented from doing so because "reselling" electricity isn't allowed in those locations. The price "per minute" is a hack to get around that restriction.