I would not want the mines hurt if it means Star Fortress gets worse mines too.
Doom is practically a capital ship in terms of power, and Alex wanted phase ships to be as strong as the next size up.
I mosly think the smaller phase ships are way more broken due to the amount of effort you need to put in to take them down.
Phase ships smaller than Doom are broken because the AI is incompetent and underperforms with them - a waste of a fleet slot that burns out PPT faster than everything else except maybe Hyperion. Only when player pilots them can he make small phase ships good. (But aside from Reaper Afflictor, I have better things to pilot, like a real capital.)
They are annoying to take down. I tend to deathball or edge-camp (and maybe send fighters) until they lose the PPT war.