You changed MAKE_SOAP to MAKE_SOAP_FAT in the permitted reactions in entity_default.txt, but didn't change the name of the reaction in reaction_other.txt. I expect this makes it impossible to actually make soap from fat. Also, it looks like you're making plant oil soap directly from the plants and lye. It seems preferable to first process the plants to oil, maybe via process to barrel? Or if they could be processed to plant oil globs with REACTION_CLASS:TALLOW, you could use the soap making reaction as is.
ATD Workshop is a terrible name. I would call it a foundry. It bothers me somewhat that you can make molds from any old junk stone. (Although it probably shouldn't, given that you can already make complex mechanical parts from stone.) Why not limit it to, say, clay and plaster type materials? And maybe sand, for simpler molds? Since you can ease the pressure on scarce bed materials with this, it seems like the required resources ought to be at least somewhat limited. (Hmm. I guess you achieve that by requiring hides, anyway.) It also kind of bothers me that you can cast magma-safe iron using only magma heat as your fuel source. And I don't understand why an anvil is required to build this workshop.
Using ITEM_TOY as a base item type for molds is clever, but it's a shame to force people out of toy making, even if it is an uncommon activity. And might a child claim a mold as a plaything? If you used, say, ITEM_TOOL instead, what problems would that cause? Maybe not stockpilable? Maybe cause adventure mode problems? It would at least make more sense for them to be tools than toys.
Casting beds is swell. Maybe furnishing them could be done at the leather works instead of the foundry itself? I don't see the point to casting querns. Casting anvils could be handy.
I quite like the gem workshop, though I might change that to "stone polisher". I also like the display case a lot. And bone blocks. And fossils.
Most of the new creatures, entities, metals, and weapons interest me less than the above items. While variety is good, it has to be balanced against the pain of scanning through expanded material lists, so I tend to pick up only those things that particularly appeal to me. Having a heavy deep material for awesome hammers sounds good for balance, but I'm not really into going after those deep materials in the first place. Calling such a material "mythril" is an instant turn-off to me, although I know a lot of other folks like that flavor. I'd probably like it better if it was produced in a reaction as something like wolfram adamantite.