I'd like to suggest adding more stonetypes that can be used for saltpeter and sulfur, you could add crystalline sulfur or sulfurous soil types and perhaps, the ability to make saltpeter via some reactions at the chemists workshop, as most saltpeter nowadays is made with other nitrates, as to the chemistry behind it, I'm uncertain of that.
You could probably do the same for sulfur, as there are a lot of rocks and metals that can have sulfur in them.
You may also want to add the ability to create your own clockwork parts, make sure it's harder to do than just killing automatons.
Aaaand, add a walking clockwork bomb creature, I'd rather fancy making a ton of them and sending them out en masse against an invading force, maybe they can use the basic landmine recipe but with the addition of clockwork parts to it.
I feel these changes would make the machine factory more useful, along with making guns more feasible.
OH, and maybe you could make stone golems or clay golems with some elixr of life or something?
Maybe some magical ingredient alternatives to the elixr as well.
Hm, yes, that sounds fun to me.
Maybe you could add some dwarven mad science like stitching together body parts and using a dwarf modified ilithid brain or two. Maybe stitching together creatures... Some other mad things, like adding wings to dogs or giving creatures the ability to shoot acid.
Stationary ilithid brain jar turrets that attack telekinetically or something.
More plants to grow into ranged attackers or stationary biters maybe.
Maybe growing your own plump helmet men and outfitting them with armor, maybe some ranged mushrooms that shoot spores to be more dwarfy than other spitting plants
A bone stone layer type for evil biomes that when mined drops bones, and maybe has small chances of creating animated bone creatures when mined, or skeltonizing gas.
Although it may be a bit out of place, you should add thermite as something you can craft, maybe you should do a whole chemistry revamp and start adding more of the periodic table (probably a lot of work, but I'd just settle for thermite)