Even in those instances, I don't think any of them happened in the last decade or two. If anything it's probably more difficult than ever to e.g. impress the right faculty member and thus bypass graduate admissions these days (Lockhart did this after meeting Erdos at Columbia in the late 80s). The amount of bureaucracy has only increased over time. More importantly much of it has been systematically automated, so you longer even have a clear system for a human to bypass a requirement in exceptional cases.
I think it's also hard to make a really good case for it. I know someone who was admitted to Harvard at 16 years old. Upon admission he already had two full years of undergraduate credit completed through a gifted youth program at Stanford. He finished his bachelors degree before he turned 18 and received his PhD at 21. He didn't "need" undergraduate education in the usual sense of the word, but he still got it (albeit in a non-traditional way) before going to grad school.
It might sound harsh but when people like that exist and still get a bachelors degree, universities don't really have to make exceptions. There's just no pressure to do so, and in their eyes anyone without the qualification is an unknown quantity with an unfamiliar bureaucratic exception process tied to it.