I have some of the same kinds of worries....my biggest doubt comes from the established canon from the Tokyopop and Archaia graphic novels--that'd be nearly $100 worth of research material to buy, and unfortunately, two of the books aren't even available on Amazon except through third-party resellers.
You don't need that manga--it's set during the Garthim wars, which is later. The creation myth graphic novels are set much earlier. The basic information is already supplied on the Dark Crystal website.
They want this set during the Gelfling Gathering, which is about 100 years after the Crystal cracks. There's a helpful timeline on the website. I think the reason they want it set during this time is because little of their existing fiction covers that time period. When I first read your post, I thought they just wanted a story that takes place in that world, but it sounds like they intentionally want something involved with those events.
That's where I have some hesitation--I'm happy to write a story set at that time, with those events happening around, but because there's not a clear beginning or ending for that time, it's more peripheral than core. We know that the Skeksis had Gelfling guards at their castle, that one of those guards discovers that the Skeksis are draining essence from Gelflings (and Podlings). This leads to the Gelfling Gathering. Up to this point, the Skeksis were believed to be benevolent rulers. The discovery by this palace guard means the Gelflings need to figure out what to do, and their seven clans unite against the Skeksis.
Later on, the Gelflings create the Wall of Destiny, the prophecy wall seen in the movie. However, that's later. The site specifies they want the novel to cover the time of the Gelfling Gathering, before the formation of the Wall of Destiny. My guess is that its creation is covered in other Dark Crystal fiction, and since this novel would be canon, they don't want contradictory stories.
So with that in mind--yay, the clans unite! It might just be me, but that's not that exciting of an ending. I'd rather write a character-focused personal story that coincides with those events, and while those events affect the character-focused story, they wouldn't be the crux of it. I'm not sure that's what the Henson company wants, but that's what I'd have to offer. The Dark Crystal fiction has a lot of interesting stuff--their world and souls are founded in music, dammit. That's fascinating, especially considering that for a thousand years, that music is wounded by the cracking of the Crystal, and it's felt in
every living thing. The world acts on a core of Harmony, so that some creatures can speak with animals, trees, rocks, not in words, but in music and music-oriented feelings. The Gelflings dreamfast--they share their memories at first touch. Despite being able to see why each other Gelfling acts the way they act, they still war with each other.
It's a world I've loved for a long time and I'm excited at the chance to make part of it. I'm gonna do what I do--if they like it, awesome for me. If not, I tried.