In Grey Gaming's video "5 Easy Ways to Fix Automatron In Fallout 4", one of the points that could be most easily rectified with a skilled mapper is an overhaul in how one traverses the Rust Devil's base. I completely agree with the youtuber's point that the pacing of the dungeon is all wrong. It would involve restructuring the entire dungeon however.
Move Jezebel's head into a "server room" where the door locks behind you after taking the head.
Make the Ahab fight the second to last encounter so you can read the terminals in the IFV room about Ahab before you fight it.
Make the Power Armor and Maintenance Room the last room with Ivey and the potentially of grabbing the leveled Power Armor before or during the boss.