Companies also use software to exert control over users and extract more money. By moving functionality from hardware into software, they can use both secrecy and laws like DMCA to restrict users' knowledge, ability, and rights to repair and modify their stuff.
The safety argument only makes any sense because so much of the system has moved from hardware into software, and this often makes the product worse, not better (e.g. your Jeep example). Compared to hardware, software is brittle, unreliable, complicated, and exploitable. However, it allows for the feature creep that marketers love and, perhaps as a byproduct or perhaps not, it transfers legal and operational control from the "owner" to the manufacturer.
If you are as committed to user freedom and well-being as you are to safety, then I urge you to modularize your vehicle design so that the safety-critical software you describe, such as auto-guidance, is completely separate from software used to, e.g., diagnose and repair mechanical problems. Then you can keep restrictions around the first kind but not the second. It sounds like, based on frustration with John Deere, you may be rewarded by the marketplace.