What part of the things you describe aren't done with the purpose of making the company money? I mean, "we're risk-averse so we force the risk onto you" is kind of the same as "we don't want to spend money so we inconvenience you".
Of course, companies are in business to make money and will tend to use whatever avenues are open. When a company starts using a monopoly position to impose legal restrictions on customers (whether to avoid risk of losing money or just to make money), sympathy for their money-making efforts tends to lessen.
Edit: Note that the approach of Deer is not warranty voiding if someone hacks the software but a license agreement which effectively terminates the ability of the farmer to use the vehicle and thus the defense above is pretty disingenuous.
See: https://www.wired.com/2015/04/dmca-ownership-john-deere/
2. What monopoly are you proposing? A monopoly on the software that comes with the tractor?
Deere effectively has a monopoly on tractors at the scale discussed in the article. That's why farmers are buying the tractors and illegally moding them rather than buying competing brands - see comments elsewhere on this page.
And, of course, they're leveraging new legal concepts which allow them to sell their tractors while maintaining control over them through software licenses.
This can also be viewed as the more general "companies act in a way that gives them the best chance of continued indeterminate existence."
Of course, most companies exist to make money. A few companies might other do good things in the mean time (go out of their way to hire under-privileged youth or something). But the assumption of liberal capitalism is that following market forces will usually do good and when it won't there are or should be laws saying otherwise.
So the "bad" companies aren't the "greedy companies" but rather those companies which either break the law or "pervert" the law - find their ways around laws that should be there or use their influence to create laws that shouldn't be there. That is, unethical corporations but not necessarily more greedy that a company hoping to make lots of money fully in the bounds of the law.
But despite this, "Corporate Greed" is shouted on the left as an objection (an objection that really makes no sense for left, right or center damn it).
And with this weak argument on the left, comes the equally disingenuous argument, "not bad because not greedy" which winds-up being a content-less defense. "What you're abusing those people but even aiming to profit by it, tell me again why this makes it OK?"
Anyway, There's nothing nefarious about protecting your profits by avoiding liability. You seem to want Deere to be this evil corporation, which simply doesn't resonate with my experience in any way.
But I do think there's a lot of room for detecting what changes were made and honoring / invalidating the warranty depending on them. Rather than simply saying "something was changed, therefore we invalidate the whole warranty."
JD has to answer to the EPA. See Tier IV.
It is highly unlikely this will work out very well for JD.
Things like ODBII Regulations, which do only Apply to Highyway Vehicles, and all of the regulations that come out of the USDOT for Highway rated Vehicles.
EDIT: By the way, I favor owner's rights (my family farms with Deere equipment, and I think there's tons of mutual advantage in open sourcing software in this case specifically and in general), but as is often the case, the "greedy corporate oppressor" narrative is too simple.