I had to leave the middle of the Welcome to the Frontier quest because of the empty spawn (no pike spawns) and then rebooted my game just to make sure. When I loaded back in and restarted the mission, the Renegade Abilities were still equipped on my character, and the game won't let me into the ship to start the mission. I tried unequipping the abilities, walking away, then re-equipping, but it still won't work. So, I cannot progress my game. Edit: I loaded back in, unequipped the abilities, quit the mission, then loaded back in. It seemed to work after I tried two more times (and changed characters). Maybe mine was just stubborn.