Ok, the good news is the flag is getting set so you don't need to redo the quest to get things fixed. I'm still looking into a way to get this to update automatically in the JS code but in the meantime there is a workaround.
1) First make sure you do not have the "Reduced Goo" or "Goo Armor Defense Drain" status effects,
2)Then go to the place on your ship where you can interact with your crew.
3) Make sure you are wearing the goo armor (not just in inventory) and interact with her.
4) In the menu choose "Customize" and make sure to use the "Exposure" tab to cover up any exposed parts and the "Style" tab to not be set to swimwear.
5) Once that is done and you exit the menu the code will automatically check for any missing upgrades and the problem should be fixed. Once it does you can re-expose body parts or do other customization as normal.