Advocates of Chesterton’s Fence tend to miss that they’re applying selective pressure to favor systems that fail to document (or outright obscure) their purpose.
Of course, the much more obvious flaw of Chesterton’s Fence is that it trivially reduces to status quo bias.
I don't think you've understood the lesson here. Chesterton's fence is not about keeping systems in place. It is about how you approach changing the system.