I wonder why the engineers didn't specify a tolerance for thickness of the oil stub pipe?

They did. Through a series of complex interactions it was missed. It’s kind of the whole point of the retrospective in the article.

per the article, because the stub pipe counter bore had to be drilled after that end of the pipe was welded in place, so directly measuring pipe wall thickness wasn't practical

Difficulty in measuring since it was machined after installation?

I wonder why you didn't read the article?