I never have enough food in the warehouse to feed my hoards, and I understand that I get coins taken to balance the shortage.  

I was wondering if there is any difference between me buying 1000 foodstuff items from the store to feed my pets (for 1000 coin) or the system charging me 1000 coin for food during reset.  

Is the system charging me 1 coin per item like the store? 

Is there any reason I should be buying from the store rather than letting the system do all the work?  Other than having enough stock for golem construction, that is.  

Thanks.

That's a good question.  I've wondered that myself, but, since the cost is the same, I just always buy the food.

I'm pretty sure there isn't a reason why you should buy the food instead of letying the system do the work, but I'd rather explore and find the food for free than have to pay 1 coin per food item.