I spent nearly 15 years in IT before returning to the family farm to work with my brothers. We farm several thousand acres of irrigated land with some large, expensive machines, so I have some experience in this. This article really hits home for me. Forgive some of the jargon, but this is slashdot; you can deal with it.
Coming from the open source world, computer technology in farming, both in the machines themselves, and the software farmers use, is like stepping back in time 20 years or more. Farm software is a niche market, and companies are pretty jealous of their profits. So mapping software is very expensive and interoperability is a bit difficult. Right now I can pull maps off my machines (Case, John Deere), but they each use different native formats so if I want to do any work in QGIS I have to use the company's individual software (which ironically enough is DRMd even though it comes for free with the machine) to export the data in SHAPE format. Software packages like the SMS mapper can read some manufacturers' data files directly because they licensed the formats. But there's very little info out there on hacking these formats and very few open source hackers know enough about farming and these systems to bring expertise to bear.
Even worse, all the companies are talking about cloud-based mapping solutions, but that's even more proprietary and closed.
Companies talk about "open standards" but what they really mean is they export SHAPE files from a computer program. It's really frustrating, but with interest in UAVs, perhaps people will finally crack this barrier.
As to the machines themselves, there are a number of issues. One is government regulations. Adjusting the timing as the farmer in the article wanted to do is extremely illegal and can get you a huge fine from the EPA if you are caught, which you will be. Because unlike in the automotive world, there aren't a any third-party repair shops with access to the parts, let alone diagnostic equipment. Apparently the EPA requires the manufacturer to report any deviations from the the approved program, and they levy fines. Sounds orwellian, but the EPA doesn't mess around when it comes to pollution regs (and I'm okay with that in theory). Suppose the manufacturers want to cover themselves.
Someone asked why a company can't spring up to develop hackable machines? There are efforts to this effect.
http://opensourceecology.org/
But for larger scale farming, it's harder. In the case of engines, the EPA would simply never allow them to market if the parameters that cause an engine to meet EPA regs are allowed to be changed. Regulatory capture has made modern diesels so expensive to develop now, including licensing patented pollution control technologies like the urea injection systems, that it's cheaper for companies to buy an existing engine than to develop their own. So even if I started a hackable tractor company I'd still need to use an engine with an extremely proprietary ECU, and would have to license canbus info to simply connect a transmission to the engine.
The other part of machines that is jealously guarded is the main canbus that links everything on the tractor. We're talking engine control, transmission control, hydraulic remotes, cab systems, and most importantly, the GPS receiver, guidance computer, and steering valve. The commands that flow on this bus are not yet encrypted (they will be soon, starting in cars I predict), but they are highly proprietary and protected by NDAs. You'd think that with a modern tractor I could take anyone's GPS receiver, mate it with anyone's guidance computer, and control any tractor's steering. Well it's not like that. On John Deere, for example, if I want to use anything other than GreenStar for GPS and guidance (a $10-$20k touch by the way, plus yearly fees for RTK), I have to physically replace the steering valve system with one that the 3rd party system is compatible with. There was a company that reverse-engineered JD's canbus commands for the GPS, and they make their own RTK GPS receiver that spoofs the original receiver to give you cheaper, more accurate positioning (maybe $5k instead of $10k). Pretty ingenious, I thought. They were sued by John Deere, but I'm not sure what happened. So far as I know they are still in business. So it is possible to route around the damage somewhat.
Physically, though, farmers are able to do a lot of repairs on machines still. On a combine, for example there are a lot of bearings, belts, hydraulic hoses, pumps, filters, and valves, all of which I can work on. So it's not all bad. Despite the computer being locked down, most of the problems I have on machines I can repair myself because they are the same problems that have happened for the last hundred years. Moving parts break and need to be welded or replaced. I've certainly done my fair share of that and saved thousands of dollars in dealer costs. Dealer charges around $200 an hour I think.