Squatting with your feet pronated will feel better because it is feeding slack to make up for compensations within the system.
Have you watched the updated Rebuilding Your Feet  series?
3 part series click the arrow on the right side of the video to #11 is part 1.
How is your ankle mobility?

A couple episodes to watch
Episode 253: Knee Pain Case Study Part 1
Episode 253: Knee Pain Case Study Part 2

Squatting with an arch is a new position squatting for you.
Rebuild your squat technique with the changed foot position. You are using muscles/tissues that weren’t being used in the past.

How are you addressing your knee?
I don’t see anything under the materials below.
Are you seeing improvement with what you are doing?