The main issue is that [ROTS] is binary, and is turned of completely by putting whatever it is in a stockpile. So really, cheese is only going to be rotting if it hasn't been stored properly. It'd be nice if we could declare separate rotting levels, like having organs rot quickly, then meat, then plants, then cheese.
And don't worry about changing something in the raws, things either go horribly wrong and force you to undo it, or they go more or less fine, and removing a [ROTS] token isn't going to be the end of the world. Mind you, this is coming from a man who just made 48 statues out of crimson banana flour gateau, worth about ☼10000 to ☼60000 each, and is probably going to get the best Goblin Diomedian Pony Christmas ever.
I don't agree. I think if something is stockpiled, we can legitimately assume the dwarves have thus prepared it and stored it in a way where it will keep, much as humans have managed for thousands of years. If you store your cheese correctly, it doesn't rot. If you store your meat correctly, it doesn't rot (dried, smoked, pickled, etc.). If your dumbass dwarfs leave it out in the magmatic heat of your fortress, or in the sun on the surface, rot will accelerate. I don't see any logical inconsistency here. So, cheese should rot unless it's in a stockpile.