IMO, this is about protection of revenue stream. Sale of the hardware is only the first transaction. Ongoing licensing and kickbacks from second-order sales is the second: bandwidth, app sales, accessories, etc.
If users modify their phone, they could possibly escape the locked-down universe this maker has created, and therefore metaphorically short-circuit revenue stream plans.
In short, it's about control. Manufacturer control of the user, but not user's control of the device. (Note I deliberately said "user" not "owner" since I believe that best reflects the viewpoint of the manufacturer.)