Funny thing, I also recalled Hexen and Doom recently as close associations to Gems of Provenance: non-linear, tangled and sometimes mazelike interconnected levels, lots of secrets (some of which are well-hidden), more or less thin story (almost absense of long readables and dialogs, the story is almost non-existent in those games and very slight in Gems), general preference of ambiance and strong environmental storytelling... In general I most like first and last levels (and also Heart and So...
I like other missions of Kung Fu Gecko (Bloodstone prison and Embracing the enemy) that he made after this one, but Library was mixed bag for me since it has hazardous combination of a) quite complicated layout which looks samey and - a bit - uninspired and b) very steep loot objective. Thankfully it was short, but his other missions are much better than this one. Though it is justified for me that it was one of the first exercises in making missions - both for author (it was his debut) and...
Good mechanists/undead horror mission. Even quite original. For me two biggest issues with this mission were: 1) too obscure and complicated objectives with vault and Amulet (ok, the last one is optional on lower difficulties) and 2) loot objective (loot is too scattered around the level - and it is major flaw of mission).
I doubt there is any cyberpunk-style missions. Only maybe some futuristic FMs like Sliptip's Kill Factory series (especially, Escape From the Planet of the Robots), or Spoonman's TSR-1000. Three Distinct Adventures by Cardia. Also, maybe, GORT's Rebellion of the Builder (hard, as I've heard).
Valky, I don't know much about Deus Ex style exactly (how it could be done in Thief) but colored lighting was implemented in Thief 2 and is in the lots of FMs for T2. Maybe I misunderstood you. As for stylistic similarities - I honestly don't know much. i've said about train mission in T2X and Konrad told you about Patriot (it's a hard campaign as I heard).
And - if you want to experience some stylistic or plot parallels between DX and Thief in Thief fan-missions (though it is really une...
I think that Purah's later missions are more advanced in almost all aspects - Calendra's Cistern in particular feels like Lampfire Hills Enhanced, but still I like Lampfire for being paradoxically both grim and cozy (even despite at same time being boxy and simplistic). Also I like how - sometimes imaginatively - this mission uses such limited space and features some vertical action.
When I find time... And I suggest you to play Heart of Bohn if you haven't yet!)) Nice mission.