TLDR: The author independently re-discovered what you may know as Old Code Syndrome. I think that's because mathematical papers place too much value on terseness and abstraction over exposition and intuition. This guy's basically in the position of a fairly new developer who's just been asked to do non-trivial update of his own code for the first time. All those clever one-liners he put into his code made him feel sm…
The problem with looking at old code is you forget what is going on or what the purpose of different components are. The problem with looking at old mathematics is that it is genuinely very difficult to understand. You work very hard to be an expert in a field and get to a level where you can read a cutting-edge research paper. Then if you let that knowledge atrophy, you won't be able to understand it without a lot of re-learning when you look at it again.
Unfortunately cute tricks like comments and concrete examples won't save you here (if concrete examples even exist -- oftentimes their constructions are so convoluted the abstract theorem is far easier to understand, and often times they are misleading. The theorem covers all cases, but all of the easily understandable concrete examples are completely trivial and don't require the theorem at all.)
Programming has existed for, say, 50-100 years. We have recorded mathematical history going back thousands, with contributions from most of the most brilliant human beings to ever exist. Do you think perhaps there's a reason why a simple and easy trick like commenting and renaming lemmas has been discovered and solidified as standard practice in programming, but hasn't been adopted in mathematics? Are mathematicians really just SO dumb?
The answer is those tricks just aren't good enough. Mathematicians do exposition. They do plenty of explaining. Any textbook and even many research papers spend a huge amount of time explaining what is going on as clearly as is possible. As it turns out the explanation helps, but the material is just plain hard.