Usually, these guys are modding the firmware to increase horsepower. Sure, I suppose in a few cases it comes down to mechanical breakdown situations, but mostly these guys are trying to squeeze out a few more horses. Last fall, my brother's JD combine started spitting up pieces of main bearings, blew the turbo. Then the rest of the engine went. $25,000.00 for a new engine and a week of down time. Turns out he had chipped the engine and the mechanic said that he had replaced 5 engines in the past weeks for similar failures - all of them chipped. I asked my brother "Why on earth would you chip such an expensive piece of equipment?" He replied that he wanted the extra 10 horses.
Having said that, there is no way that JD should be able to control the owner of the equipment in the fashion that they do. If the farmers want to mod, they should be able to. Whether it's a good idea or not. It should be the owner's decision.