I think that Ill-advised modifications is bad enough that any ship with it is entirely useless. I haven't seen a single ship with this that was a threat.
Irregardless, I think it needs some changes to make it actually usable, instead of just, The ship shuts down as soon as the battle starts.
give it these effects
Between 80% and 100% shorter Peak Performance Time
+100-200% CR degredation.
Always Degrades in combat.
+300% (or so) CR Recovery rate. (no increase in supply cost)
Or any combination thereof (and with any actual values)
The effect would be, This ship works great, for a very short time. Like 30 seconds at best. A typical CR timer of 3 minutes would drop to 36 seconds. After it starts degrading, it degrades fast. As such, once it hits the Degredation stage, it rapidly falls into the Low CR.
This would give a short window where such a ship functions, after which it goes into the Low-No CR state, at which point it behaves quite a bit like it does currently.
In addition, it is fast to restore to combat condition afterwards.