I think I'd prefer if Nihilo was reserved for very rare materials. A way to find things like Kaolinite and Graphite, maybe some of the higher tier materials. If you made it require wood blocks(TFC wood blocks, the ones you craft with planks), that requires you to have a saw, which at least requires you to have metal, so you couldn't chop down a tree and kill a few spiders and have metal production going in a few hours.
Edit: You could also require a Sieve to have something higher-tier in it's construction. Maybe it needs a 'wool net' or something instead of the spider one, which requires you to spin yarn which means you have to have cloth production. Just an idea.
Also since you can config Sieves to require certain materials, or only work for certain items, it would be possible for you to limit their use to only the types of rock/dirt/cobble/gravel/sand that the material you want spawns on(For example, Kaolinite only spawns in Sedimentary Stone).
Basically my 'ideal' for something like the Ex Nihilo Sieve would be a bit like an 'unlimited, targetted' Sluice. Something you could use to augment your metal/mineral mining, rather than replace it. And I'd also remove all the options to automate it.
I've actually been trying to config Ex Nihilo to work with TFC for that exact purpose, to act as a way to find certain rarer materials without wandering a world fruitlessly for multiple real-world days, because having literally everything necessary for metalworking -except- a crucible is incredibly frustrating, and leaves your entire progression up to RNG- which isn't fun at all.
There's also an argument for making these results with a Sieve very rare, but if you're resorting to a completely un-automatable thing like a Sieve(if you turn off automation, anyway) to get these materials, I don't believe it's necessary to further punish someone by making the material they're looking for extremely rare. it shouldn't be particularly common but I don't think it's desirable to force them to Sieve 1,000 blocks for 1 piece of Kaolinite, for example.
Also I would like to say that I would absolutely adore a TerraFirmaCraft Skyblock.
Nihilo Barrels are sort of redundant, TFC barrels are better in basically every way, outside of the rare materials I mentioned(like Soul Sand or Spawning Endermen or something like that). Maybe disable the uses of them that aren't for getting these rarer materials?
Crucibles... I'm not sure what you should do with the crucibles, to be completely honest with you. I'd almost say to disable them, remove the recipe, because I can't think of anything they do that you'd want people to be able to do as early as a Crucible would allow.
Most of the other stuff seems fine, you could add ore doubling in a very slow way with the way that you can crush ores down from Gravel > Sand > Dust, maybe that'd be acceptable?
Basically I think the role that Ex Nihilo/Aquilo should fill in a TFC-type pack would be a stopgap for people hurting for rarer materials, not a replacement for normal material gathering. If that makes sense?