It is mostly a matter of scale when it comes to the actual farm operations. Larger operations have the available capital to invest in pricy equipment that decreases their operational expenses (favorable tax advantages make this a win for most businesses, bug operations just have the cash/credit to actually act upon the available options.) For a farm a lot of that expense is fuel, fertilizer, and herbicide/pesticide; larger, more efficient equipment is usually the quickest route to being fuel efficient on the farm and there are a variety of options ranging from GMO crops to smarter tilling and cover crops to try to reduce the usage of fertilizer and other chemicals. A lot of these techniques were pioneered or "re-discovered" by modern organic farming but the make sense for any farm.
As for the efficiencies in transportation, a recent book to take on that subject was "Just Food: Where Locovores Got It Wrong". The basic idea, which makes a lot of sense when you think about it, is that modern logistics systems have spent a lot of time and research on getting very good at what they do. Companies in this business track every penny involved in getting goods from point A to a lot of different point Bs. One big truck going from the farm to a regional distribution center and then twenty smaller trucks going shorter distances from that center to customers ends up being a lot more efficient than a small army of trucks going from the farms to those twenty customer sites.
There are some externalities that do not show up on the bottom line, but I can't see it being more than a drop in the bucket compared to the total cost of the entire effort.