You are comparing big teams and products to a single guy writing a paper intended for a niche audience and to be read maybe a few hundred times if he is lucky. People makes mistakes and sometimes forget to document everything, they try to document everything though as can be seen in their papers where most things are documented well, but sometimes they miss things and unlike code you don't have compiler warnings telling you about it. And given how few people read those papers it isn't worth investing in a team to go through and update all of those papers to properly add definitions for everything they missed.

The equivalent to those programs in math would be high school textbooks, and they are extremely well documented and easy to read in most cases.