> always starting with a reference design and tweaking from there.

That's just basic design sensibilities.

There's a big difference between a human looking at a datasheet and manually copying the reference design (possibly leaving out things like pullups because they're simple/obvious/etc, or go to a different block of the circuit than what you're focusing on), and a mechanical copy with the pullup resistor only possibly being deleted after an explicit reasoning step focused on it.

In the given example, the human process obviously failed, right?