I've always believed that the largest ship in the Imperium is 1,000,000T.
It quite possibly is. I'm going off of memory which is quite possibly faulty.
. . .It does sound like a ridiculously large ship, even if three quarters of it goes to drives and fuel tanks. OTOH, perhaps the main point is that it's larger than any other yacht. The Imperium's billionaires have had yachts built for them for over a millenium (or call it half a millenium if you think the Civil War somehow "reset" the playing field). If every few years some billionaire orders a yacht that's bigger than anything else built so far, you could get quite a bit of size inflation in that time.
That is, almost certainly, the reason you would have such a large yacht. It would simply be a vanity for the head of some megacorp that their yacht is bigger than anyone else's. The actual need for a ship that size has nothing to do with it.
But several thousand dT of 'payload'? What would the naval architect spend that volume on?
(One idea just occurred to me: A big garden or park. Perhaps even a hunnting preserve.)
Try looking at information about the largest yachts in the world for ideas. It would probably have multiple 'launches' such as practical launches used by the crew for supplies and the like as well as private 'launches' that are similar vanities such as a 200 dton 'safari launch'.
While I suspect that 25,000 (or even 50,000 tons) is probably not enough space for a real hunting preserve there are still plenty of things that you could put on such a yacht that would fill up a lot of your space. While normal spaceships are designed with a high degree of efficiency of space such a yacht would be doing almost the opposite, using as much space as possible simply to help justify why it was built so large. This would include things like not only a dining room but also a kitchen, two things not normally found on a ship. You would probably also have a ballroom, a study, an entertainment room, etc.. Look at large mansions for examples of such rooms you might want to add.
If you are still trying to take up space you can separate off part of the ship as 'office space'. There's no reason such a rich person has to be attending to business in his study. Setting aside part of the ship for his office, the quarters for his secretarial staff (who are different from his personal staff), with their own private dining areas, kitchens, and lounges.
Such a huge ship will also have a lot of staff. You will want enough engineers for 3 shifts. You will need command crew for three shifts as well. While such a ship will almost certainly not have 1 turret per 100 tons it will still have some turrets in order to keep it from becoming too tempting a target. That will require a gunner per turret. There will also almost certainly be a security staff on board. All of this will require a medical staff. And then, of course, there's going to be huge amounts of stewards. You will need stewards to prepare the food for all these people, stewards to keep the hallways and common areas of the offices and crew areas clean, and then of course more than the normal compliment of stewards for your guests and cleaning of the 'living' areas.
With so many servants they will probably have their own eating areas. After all, you don't want them using the dining room. It wouldn't even be that unlikely that there are multiple eating areas for the different 'groups' of servants; 'crew' eating in one area, business personnel eating in another, and 'staff' (meaning stewards and junior officers) in a third. And of course those areas may require their own kitchens (though that isn't mandatory if the main kitchen is placed in a junction of areas). You could look towards period pieces such as Upstair, Downstair or the more recent Downton Abbey for ideas about how the differing groups of 'servants' might be separated.
Perhaps I should go with the largest passenger liners instead?
There's a bit more ease to that because you don't have to worry as much about the 'organic' functions of the ship, but in many ways there probably isn't a huge amount of difference in the two. You are simply replacing 'guest rooms' with 'passenger quarters'. It's a little easier because the rooms can be much more modular and you don't have to worry as much about some of the 'living spaces' such as a study or conservatory, but to make a passenger liner more 'real' you have to go back to giving more thought about space efficiency. After all, a passenger liner is designed to make money and wasted space is lost money. On the other hand a yacht, especially like one you are talking about, is almost by its nature designed to be inefficient with its space (you would probably see some issues of efficiency in the crew, staff, and business personnel just so that more space could be used by the owner and guests, but it would probably be far less than you would see on something such as a scout ship or cargo ship).
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