[eridius]

Huh, I only ever heard people mentioning this issue for 10.11. Never heard about it at all when 10.10 came out. I bet that's why I never saw any explanation for this reason, because people who had heard about this with 10.10 were just assuming that's what was going on.

Incidentally, I had no idea about ⌘L to show logs during OS update.

In any case, even if the OS update takes a long time, the end result is you still have the same /usr/local you did before.

Also, FWIW, the discussion you linked to references TeXLive, as does the blog post you linked. I wonder if the issue here is not in fact having anything in /usr/local, but rather having used a package installer to install something into /usr/local (which I assume TeXLive does). It doesn't make much sense to me for the OS updater to move everything out of /usr/local and then back in one-by-one under normal conditions. But if you used a package installer to install into /usr/local, then it would make more sense for it to do something like that (which is to say, it may have special behavior around things covered by package receipts).

Edit: Well, under normal conditions, it might still move the folder away and back, but I'd expect it to just move all the top-level items from the folder back, instead of manually copying all of the nested files).