I really wish I new this before I had actually gotten the ship.
Tip to Obtain Pra Mah Ship
Get The Rewinder Weapon
This weapon right here.
Use it to shoot the beacon things the Pra Mah ships have placed at the beginning of the fight.
It will teleport the beacons away into the abyss presumably. This is probably unintentional so abuse it while it lasts. I wish I had known this when I was trying to get the ship on hard.