I know exactly how this got created. First of all, these maps were made back in the day using old versions of Unreal, not january 1998 as the current usp review claims, they also don't have the svalley1 fix there as that map tends to crash on modern versions of Unreal due to ai paths not being built properly (this wasn't an issue with the old version it was made on btw).
In fact the svalley1 fix seems to be hard to find now that I am looking for it. I also disagree about the statement that the other maps weren't made because from what I've once heard, they were, he just either didn't release them to general public or it was on some obscure site and got lost just like many other things.
And I know that shamuquest 2 was intended as a prequel not a remake....kind of like those star wars episodes thing. http://www.unrealsp.org/legacy/?q=reviewshttp://www.unrealsp.org/legacy/communit ... quest.html
But to get back about that brush: That was normal back in the day. People couldn't create terrains etc easily back then. So there was a lot of intersecting and brush cutting and this is how it came out.
Jeff Rubin did the same thing when working on Unreal PSX, just check some of his brushes and indeed the maps are nightmare to work with....
So really, this kind of stuff used to be acceptable.
EDIT: Just in case, I say it but in Dig by Cliff, there are similarly made shapes, not broken that much mind you and done with more care, but they have been also shaped out using the intersect/deintersect and sometimes gained odd polys.