Thanks everybody for being very constructive and helping me with the story.
I like the idea that the throne is really old, so maybe it was indeed "aulde Tau technologys", now forgotten - maybe there is some Tau equivalent (sort of, obviously the lesser thing, and maybe only insofar as Space Travel signalling goes with the Elerium and such) so thanks to Kage for that one.
The description of a one-entry only restricted area of the ship for the Navigators aka the Sanctum I found very evocative and I will include that one, so thanks tp SpawnoChaos.
Cifer's idea about either or the Sanctum / tank having social implications is attractive, too, especially the corruption/inbreeding/mutation issue. I also like the Rogue Trader's take on navigation, so that maybe the longer you're on the job, the weirder you go, and maybe the Elerium is some sort of catalyst/hook like the Spice in Dune. Experienced navigators can ingest/immerse themselves in bigger quantities and perform safer jumps/quicker/longer. Being good old catch-22 WH40K, apart from the price there is most certainly a horizon in that ability. So at some point the jumps get more difficult/ attract more Warp creatures as the Navigator thins the veil between himself and Chaos.
My planned campaign should feature some 10 or so installments ( I have always done unending campaigns, and I would like to limit the whole arc). I want it to portray the liberation of a (Tau) prisoner from an inquisition prison, not necessarily with force, an exchange of the Tau for the refining instructions for the Elerium, that are so tremendous that the PC should figure out themselves that they will require the uses of an entire Forge World for several years ( I gave all PC two campaign secrets to start with, and here I planned the hint "time has a different meaning for Space Marines when building things" to interlock so that the players can realize it's no problem if they spend five years on that manufacturing job), obviously requiring some muscle on their part to get the production running on their terms. A ancient manuscript will play a role, and a group of people that are also, maybe unknowingly, involved in thwarting the heroes, that will have no idea on what it actually is that they are manufacturing.
One of the installments will involve a member of the Adeptus Custodes to come get the fluid, at which point the players ultimately should get the idea of what the point is of the mini-series. I hope they don't get it until then, and that I can leave enough breadcrumbs that it all makes sense in the end, which might be difficult.
Further ideas, non-ordered:
PCs get orders from "the Concilum", a secret body within the Deathwatch, and they will later reveal that the Council is composed of three people, the "Allfather", a mystical man, probably a very old Space Marine, "Mother", some form of artifcial intelligence and one of the High Lords of Terra.
I am still working on ordering the components and making them interlinked, which I find the hardest work. Anyway, I hope that we actually get to play the thing, all of us getting, well, kinda old and having families and day jobs.....
Once again, thanks everybody for helping with the story, if anything in here piques your interest and you would like to suggest, elaborate or criticize, you are most welcome to do so.