So I dealt the final shot to the boss, when it jumped away. Is this preventable by taking out the engines or pilot station?

And how the hell does it repair its hull up to full strength without any bases?

Nope

The boss is set to a fixed number of stages (won't tell how many in case you still haven't beat the game), so the escape+hull repair are scripted.

Even killing the crew, won't win you the battle.

The story behind the hull repair is that it breaks off a whole part of the ship each battle, so the next battle is with the still intact remaining parts of the ship. So it does not really repair, the hull bars are for each part of the ship. Thats my own speculation,though.

To bad its scripted :(.

Benice to at least have ONE strategy to kill it before it runs off.

Killing all crew and destroying the engines does not stop it, sadly :(