The Chesterton fence in my book is only about something that is still meaningful only in non-obvious ways. In evolutionary theory I believe "used to have a sensible explanation but no longer does due to changing circumstances" is known as discordance.
The fence is about all things that you might want to change, whether or not they're still useful. Both of the characters in Chesterton's parable are reformers, and the assumption is still that the goal should be reform. The question is more about the motivation for reform.
The first character wishes to remove the fence because they don't see a good reason for it. The second takes a different approach: first show that it isn't necessary, then remove it.
Plenty of things are made useless over time. But there are also lots of things that look useless but aren't. We don't know, a priori, which is which, hence the need to be cautious.
(That said, I think there are also cases where ignoring Chesterton, removing the fence, and seeing what will happen is the best option. It just requires good planning and good testing so that you can be confident that a bull doesn't suddenly appear out of nowhere!)
