The automation has been around since old MDF, and sort of makes sense. Its not like relics, fossils, and chests are good for much else, and I think some races have or used to have reactions that scoop up any old raw gem (which might include the Archeology stuff), so its best they get cashed in before your dudes accidentally use them for something silly. Sort of how the loom grabs all usable thread automatically so that your doctors don't use the dyed silk instead of the horse hair for stitches.
As for what I was thinking, I agree that the Orcs should have the archaeology workshop back, if that is not the case, I would rather bundle the use of fossils, relics, and old chests into existing Orc Workshops.
For Example:
Draw Metals from Fossil: Amostubal's proposed reaction, requiring a Fossil, barrel of blood, bar of ash, and unit of bonemeal. Preformed at the Boneforge
Commission Necromancers to Reanimate Fossil: Done at the Shadowbroker, requiring a fossil and alot of platinum. Adds some sort of evil semi-undead monster to your fort as a pet.
Handcraft Sacred Gear: Performed at the Tribal Wargear with a relic and the standard handcrafted bonemold fixings. These reactions could make items out of the procedurally generated divine metals, or high grade Dreamwalker magic stuff once that is fully implemented again.
Defile Sacred Remains: Performed at the Dismemberment Theater at the cost of a Relic. Provides a huge boost to diagnostic skill, some bonemeal, and curses the orc who preformed the interaction as if they had angered a god. (Good for invoking fun or trying to build vampire forts)
Enshrine Sacred Remains: Performed at the Carpentry or Masonry Workshop with a Wood or Stone Coffin and a relic. Produces a very valuable piece of decorative furniture (perhaps a statue) called a Shrine.
Ransom Relic to the Church: Performed at the Shadowbroker. Trade a Relic for a Ship full of Abbey loot, or perhaps some platinum.
Goblins Tinker with Contents of Old Chest: Performed at the Tinker with an Old Chest, Two Mechanisms, a Brass Bar, a Steel Bar, and some Potash. Provides a windfall of guns, bullets, and advanced trap components made from Deep Bronze and other such rare metals.
Refine Ancient Metals from Contents of Old Chest: Spend a handful of Bronze and Steel with an Old Chest and Fuel to make a bunch of Orchialcum and Deep Bronze at the Ancient Foundry.