I think the majority of modifications are simply adjusting the calibration or lookup tables for things like fuel maps, enabling / disabling things like key left in ignition buzzers and the like, mostly data items rather than code modifications. There may be more adventurous modifications like adding launch control to a performance cars, but that may just be enabling existing code rather than adding new code.
My cars are old (1998) Nissan Skylines, who's ECUs are pretty basic, asides from killing the engine there's not much you can do to cause more issue than a mechanical modification like adding a larger turbo, or maintenance neglect. The ABS and traction control are handled by physically separate ECUs, though I imagine things are more integrated in the main drive train ECU in modern cars.
While I haven't modified the existing or written my own firmware to load on the ECU that mostly due to lack of time, one of them came from Japan with a Piggy Back ECU installed which intercepts the inputs / outputs to override the mapping of the OEM ECU to tune for other mechanical modifications. An alternative is to buy an aftermarket ECU or build a custom one, those tend to have less integrated safety features (stability control, etc.) than the OEM ones and integrate less well with the car's other systems, I'd expect them to cause more issues overall than relatively simple modifications of the OEM firmware.
I'm sure there are extremes where people may cause problems, but this kind of thing has been happening since cars have had computers so I doubt there's any great calamity around the corner.