I can see why its battleship sized. Maybe there are only 10,000 psykers on board. But I suspect we are talking about alot of high level psykers, and we know the Imperium's outlook towards them. I suspect whole segments of deck could be taken up by one holding facility of a high level psyker.
Lots of hull mass being dedicated to isolation, seperation, sororitas barracks, checkpoints, dampening fields, etc. A super prison, with all dedicated to keeping those that are in, in, and keeping those that are out, out.
If there are only a handful of these in the galaxy, I can see them existing. As to risking warp loss, it would be a tragedy to lose it, but from the fluff it seems these things are practically bombarded with holy wards and obviously a super gellar field they won't enter warp without.
Its supposed to be a fortress. Ok. But I'm thinking, isnt a normal battleship brimming with as much defenses as can be had?
Well you can say, there are only a handful of these ships, and yes, they are entirely impractical for cost/benefit but they have a very special purpose.
Alright, but I do have issue then with them spending power on battleship range weapons. Their escort fleet should do most of the heavy lifting.
I say, keep the defensive stats as is, even make it 6+ all around. But no more than cruiser level firepower, battlecruiser at the MOST.
And nothing above 30cm. That would be a highly specialized ship I could get behind.