Air attacks can do 3 suppression iirc, it's just rare.

but if you want to edit the percentages:
Unity of Command 2\_packages\base\config\Game.yml

This is correct. Your mod need only contain the file:

config/game.patch.yml

This file should contain just the (two, I think) lines from game.yml which define the air attack and suppression damage. In there, change the original value to the values you think are appropriate.

Are these the 2 lines? I just need to change the values all to 3?

# Air attacks
normal_sup_table: [0, 0, 0, 0, 1, 2, 3, 0, 0, 0]

What determines if an Air Attack kills or suppresses?

You need these two lines.

Change all values to 3 in the sup table, and change all values to 0 in the kia table. This will make air attacks always suppress 3 steps, regardless of shifts (weather etc).

To better understand the lines: you can find them in the manual section 3.9. where it explains how they work.