The major difficulty (well, relative to the other work involved) is figuring out what to do with the fertiliser once it’s in the game. Adding a new recipe and item is one thing; but changing the vanilla crop growth gets trickier…
Sure, the obvious choice is that it somehow speeds up crop growth, so that seems like just a simple value change. However, that means hooking into all the existing data relating to crops, trying to find something that works nicely and will be compatible with other changes to those crops… there’s a good reason that modders generally try to avoid changing vanilla content, unless there’s an obvious lack of a feature or a simple way to keep their mod as a pure “add-on” rather than any kind of overwrite.
That’s not to say that it couldn’t be done, and the last thing I want to do is shoot down the idea. However, for a feature like this to really be useful, it would be better as part of the vanilla game. Then, modders could add all kinds of cool stuff around fertilisers and soil conditioning and so on; without having to worry about compatability since they’d only be adding to vanilla content rather than changing any of it.
There are other options, such as using compost + crop output (representing seeds) + clay pot or trough to make a planter, which is later harvested to return an empty pot/trough and 2+ of the output crop… and while options like that can have additional functions and benefits (grow your crops anywhere in a greenhouse!), they can feel kind of tacked-on.
The thing is, Radiant already plan to come back to crops and farming and soil conditioning at some later stage. I’d say that, until then, any modding attempt to achieve the same result is going to be restricted to being a poorer substitute, simply because there are limitations for modders that the Devs don’t have to worry about as much.
Buuuuut, that’s not to say that modding things with the rotten food isn’t worth doing… I’m simply suggesting it may be better to look at other avenues to fertiliser. For example, we have turnip shooters… imagine shooting rotten turnips and other rotten vegetables instead? Maybe they don’t do as much damage (so they don’t replace/overpower the vanilla version), but they could give some other debuff such as scattering enemies because they can’t stand the horrible smell?
Or, how about leaving a pile of rotten food out long enough has a small chance to attract rats? And not just normal rats, once the “scouts” discover a food supply their bigger cousins could follow… and then you need to send someone to deal with the Giant Rats around the place, and you better have an Herbalist on hand in case any of them get bitten and contract the deadly Rat Plague (and yes, I know it was actually fleas on the rats that carried plagues, but I’m gamifying it 
)
My point here is simply that, especially in this early stage, additions generally work better for mods than tweaks do. If some modder wants to take the time to keep such a tweak-based mod up to date, that’s awesome and I’m sure it would be used by many players. But, most modders only have a limited time they can focus on it, and already have too many ideas crowding around waiting to get out… so, making additions which are easier to maintain leaves more time for actually creating things. That’s why I’d say it’s probably easier to organise a new content mod which adds to the gameplay, rather than a tweak mod which goes back to edit existing things.
