In the end it's about the emergent stories it creates. If the system is just sunk complexity everybody will ignore it until it becomes a micromanagement problem, or just work around it (eggs anyone?).
AFAIK nobody has suggested that farmland could spawn non-vermin creatures. Stuff like, plump helmet men or giant moths. Unexperienced farmers wouldn't notice there's anything wrong with the plant when harvesting, then go store those spawns in inconvenient places where there may be no proper containment.
You might actually be interested in the
Xenosynthesis side-suggestion, which tries to weave this together with the magic biome concept (that are supposed to replace good and evil biomes eventually). Part of the point is that messing with magic would cause all sorts of life-forms to become magically altered, and a negative consequence like this could be a possible result.
As for the emergent storytelling question...
Well, how much does needing to dig out a space for stockpiles and workshops or circumvent an aquifer or set up training for military lead to emergent stories
on its own?
How much does the fact that you have to do these things change the character of the emergent stories compared to if you didn't have to actually excavate, build, or work towards training dwarves?
Part of the idea I'm trying to convey with farming is that it's a foundational building block of how we solve all tasks in the game. You can make combat "harder" by adding larger, stronger monsters to fight, or you can make combat "harder" by not having steel weapons readily available, by making training military dwarves up to legendary skill levels significantly more difficult, or otherwise taking away some of the advantages that people take for granted.
If farming changes mean that you have to have an open-air orchard that leaves you more exposed to sieges, then "building an orchard" doesn't make an emergent story in and of itself, but it does severely change the way that those emergent stories about sieges or flying enemies turn out.
And besides that... isn't the whole point of
emergent storytelling that it's not something strictly planned for? It's something that springs up from interactive game elements that alter one another in unexpected ways. Toady never
planned on Boatmurder solutions to sieges or that they would lead to burning socks that kill a whole fortress. That was an emergent story that arose out of an emergent gameplay technique that caused an unforeseen consequence.
The only way to plan for emergent gameplay and storytelling is to create more interconnected gameplay mechanics that can cause such emergent behavior to arise. Water flows are a big part of this specifically because engineering how water moves is something that plays upon one of DF's great strengths in the player's capacity to control the flow of water through emergent gameplay techniques. There is also the use of fertilizers, based upon either manure collection or killing, decomposing, and transporting biological waste to the farms, all of which are a good source of emergent logistic techniques, including minecarts and drawbridge catapults. Beyond that, the entire polyculture concept is based around letting crops interact with one another in potentially unexpected ways, especially if you include the part where the crops can be procedurally generated at worldgen each time. ("It turns out that when you plant 'flaming trouser kumquats' with 'stinky matted bushes', they produce food while only needing a small supply of my mashed kitten fertilizers and water!")