Don't need a rebalance, every ship has different benefits and quirks, it gives them flavor. Balance them as many would see fit and we have many ships all the same. BORING
It's not a case of balancing so they're "all the same".
It's about balancing them so each one performs consistently based on it's components.
A light ship should be faster than a heavy ship with the same thrusters.
A small ship should have better defences than a larger ship with the same shields.
A light ship should have lower integrity than a heavier ship of similar size.
Similar sized ships should be similar weights.
Once you've done that, then (if necessary) you could give ships unique features by allowing them to fit better modules.
That's got to be preferable to making certain ships superior as a result of magical statistical pixie-dust.