Rot is, at its core, not enough of an influence except a small incentive to sell/buy food quicker.
I disagree, completely. I think your method does not address the realities of how food is actually handled on Dwilight. Until you've actually had to manage a city, or possibly a townsland, on Dwilight I don't think you can really know how it works.
I ran some quick numbers myself, based on the following assumptions:
1) A city that consumes 60 food per day. (i.e. it has to remove 60 bushels from the warehouse per day.)
2) All food is stored in warehouses, and subject to 1% rot per day.
3) On the first day of Winter, the city has enough food stored to feed itself through the entire winter period. This is how things usually work. You normally do not manage to buy food during the winter. But even if you do, then due to the low production of all regions, the food you buy was harvested in Autumn, and has been sitting in someone else's warehouse rotting away since then. So it rots one way or the other.
We start with 1200 bushels. After 21 days, we have lost only 111 bushels to rot, or 9.3%. No too bad. But any city lord who only stocks enough food to get him through the Winter is in for a world of hurt when no one will sell him food come spring time. And they won't, because they will need that food themselves.
So let's modify our original assumptions to stipulate that we stockpile enough food to last us through the end of Spring. This is a more realistic scenario, as it takes time for the lightly increased spring harvests to build up enough reserves to let the regions start selling. And you need reserves to make sure that you have enough time to actually buy it, in case someone else gets the first few sell orders.
In order to get through all of winter and spring, the city needs to stockpile
3200 bushels. Of that total, a whopping 648 bushels will rot away or
20.3% of your stockpile.
Stockpiling enough food to last that long is not out of the ordinary. Nor will any city lord think it overly excessive. Nor will any sane city lord routinely maintain a situation where his city has only 6 or 7 days of food in stock, if he can possibly help it. (Note that this is for Dwilight, where it can often be hard to come by food. Other island may vary.) You want at least two weeks of food on hand at all times in case of emergencies.
Also, note that the 20.3% rot only counts food for that half of the year. I haven't tried to deal with the rest of the year. But that will only make the total rot figure go up even higher.
The way in which winter affects the handling and stockpiling of food makes rot much more significant that you're making it out to be. I may be exaggerating a bit, but I don't think that anyone who plays a margrave of a city on Dwilight will find too much fault with my assumptions here.