Operational Funds?

There's a patreon?

Possibly but where did all the stuff in the captains quarters come from none of that seems standard issue does it?

Hmm, if I understand the question correctly: When you're talking about something like the Alliance/Alliant you have to think way up in scale. Their population across hundreds of core worlds and tens of thousands of colonies would be in the trillions, and while more or less every habitable world is on or near the wormhole network, you still have to traverse areas of space within the individual systems using conventional light speed limited physics. (Assuming you don't have something on the ship that can warp space-time for you, like say a singularity drive.)

This is why Zephyr was caught totally off-guard by the Ashtor fleet coming out of the dark of space rather than through the wormholes. It is also why the enemy fleet in book 2 can still see the Sheol even though it had a significant head start. They hadn't actually gotten all that far away in the context of what sensors can pick up in a system. The subtext in the book was that Greye knew he couldn't go to the wormholes because the Alliant would nab him immediately, but if he goes straight out into space, the ship not being in sufficient repair to self-sustain would eventually kill them as well. I try to convey his stress about that, but it is a bit overshadowed by the incoming fleet and the violence onboard with the Cutter uprising. It is there, though.

Anyway, I say all that to say that a centralized government operating an economy that is that complex and spread out in such circumstances would be even more disastrous than it is when people try to pull it off on just our own planet, so the Alliant would undoubtedly be using local contractors for just about everything, with a little more consolidated control on worlds like Zephyr where you have a military ship yard (IE the Orbital Ring that the Ashtor target first and successfully destroy).

That being said, molecular printers are also a thing and they do fit inside the larger ships like the Megaliths, so you can probably print your own desks if you need to. But consumables like paper towels would benefit from machinery designed to scale production specifically to that good.

As for the Sheol specifically, they're cut off from the galactic economy more or less as a whole, so they'll have to make do with what they can get. (Although if you have a forest the size of a national park inside said ship and a working population, who's to say you couldn't eventually set up your own paper mill? Or go even easier and faster and do it with hemp?)

Sci-fi is a fun genre. :P