@Jeffro -

But it’s just bad practice to make modifications like that as it ruins the upgrade path.

But that's the point, isn't it? Not everyone wants to maintain the upgrade path. They intentionally fork, in essence, to make WordPress suit their purposes.

Granted, such users are a minuscule subset of the WordPress userbase. But they do exist. One such member even participates - or, used to - in the Tavern Forum.