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Universe class has a passenger complement of 200000-500000. This is huge. Is there any info on whether these ships are able to / have been used to transport Imperium's troops?

Well, since you've got capacity #s, I'd assume the answer is YES - even if there's no specific in-print examples to point you to. Afterall, the whole point of 40k is the battles. So there'd be no reason to tell you about that detail unless it fed back into the fighting.

Have GW even mentioned this ship, outside of the Rogue Trader RPG?

I think one is dispatched by the Adeptus Mechanicus to transport a load of Imperial Guard regiments after they saved Fortis Binary Forge World in the Gaunt's Ghosts books

I think in One of the Ghaunts Ghosts novels they ride in a requisisioned freighter

Mass conveyors are a lot bigger than 'normal' freighters.
The misericorde from dark heresy is another example.

The Imperium can use them on war zones but wouldn't like to do so - they're basically defenceless, slow as hell in real space, and represent a huge chunk of the economy of the sector you take them from, and are often old borderline archeotech.

So I'm sure the Imperium would, but it'd rather use an equivalent number of 'normal' freighters - their loss is less catastrophic, they can be in more places at once, and they can scatter and run if a convoy escort destroyed.

But sometimes needs must.

Even with the Imperium's disregard for lives, I'm pretty sure someone along the chain of command would object to putting that many eggs in one basket.

Tygre wrote:
Have GW even mentioned this ship, outside of the Rogue Trader RPG?

Yes. A convoy of ten Mass Conveyors were lost to a Necron raising. It was in one of the detailed factbooks, I think a forgeworld book rather than a Necron codex, but official stuff.
Sorry, but I cant remember where I read this.

It's worth noting that the crew/passenger complements of the ships given in Rogue Trader RPG are orders of magnitude larger than all of the BFG information. It looks like the author just went with 'slap some extra zeros on the end because EPIC!'