I've figured out a workaround until the modder decides to update the mod.

Step 1 : Go into your "steamapps>common>Starbound>storage>player" folder, find the 2 files related to your Boss Monster(PLAYER file, SHIPWORLD file, if you're having trouble finding them then hop into starbound and try to load up your boss monster character, task manager the game and then check which files are the most recently updated).

Step 1.b : You might want to backup your entire Player folder if you either aren't familiar with what you're doing or have a LOT of Starbound characters

Step 2 : move everything that isn't those files and the metadata and statistics files out to a new folder for temporary storage

Step 3 : Start a new character(One that isn't a boss monster) and progress to the post-repaired-ship stage(/admin is recommended, as you'll have to fight with your starter gear)

Step 4 : close starbound and find the new files relating to your new character, delete their .player file but move their .shipworld out of the folder

Step 5 : Rename your new character's .shipworld to the same name as your glitched Boss Monster's shipworld file, copy it back into the folder and boot up your Boss Monster
If it all worked you'll load in with whatever ship you had on your new character, but you'll be your boss monster again!

Step 5.b : Once you've got it to work feel free to move your other saves back into the folder as there's no longer any risk of collateral damage
Hope this helped!

EDIT: I haven't tried this personally, but i'd suspect that upgrading your ship as a boss monster might break it again, if that's the case you'll have to go make another character and progress to the point where you've got the same level upgraded ship and then do the above steps of overwriting the .shipworld file of your boss monster again.

EDIT:Turns out you can't actually fly your ship, not even if you spawn in and place the item "Boss Monstercaptainschair", it's a bit depressing, but nothing a good ol' bit of modding can't fix

If you have any issues or questions, feel free to post it and i'll try to get to it as soon as i can