They fall within the realm of normal, intended DM prerogative.
Most DMs would only adopt one or two optional rules, making it feel largely as intended with a slight tweak. This is a host of optional rules, combined with lots of things way outside those, and adding a ton of changes after. "DM prerogative" is being so loosely interpreted here that we could say writing an entirely new rules system would count as "DM prerogative".
