The problems arise when you have to combine code from 
  different repositories into a single deployable product. 

OK, we only have a single deployable product, which combines code from all those repositories, so it seems we match this criterion.

  But when you store those libraries in separate repositories, it 
  becomes impossible to describe the state of your deployed code 
  without listing the version of every single dependency. 

Yes, and that is what we do: each released lib has a version. The deployed version only uses released libs and lists exactly what it uses. The libs cannot be overwritten or changed after release: once released, that's what that version of the lib is.

  [..]
  If everything lives in the same tree, then a single commit ID 
  reproducibly describes a complete system from top to bottom. 

In our case a single commit ID also reproducibly describes what has been deployed. Each library version was built from a specific commit ID in their respective repos.

  And you can atomically make changes that cross module 
  boundaries, which is difficult to do safely with separate 
  repositories.

We don't have to atomically change anything, because a new backwards incompatible release of a certain lib doesn't affect any other lib, until we explicitly opt to upgrade it to the new version and release a new version. And if it's backwards compatible, it gets automatically picked up, because version management allows it.

So I just don't recognize any of: I don't want to waste time dealing with multiple commands to manage multiple repositories. I don't want to waste time or expend cognitive load dealing with submodule, subrepository, or big files management. I don't want to waste time trying to find and reuse code, data, or documentation. I want everything at my fingertips, where it can be easily discovered, inspected, and used.

I have a directory with a tree of repos. They could be in one big repo, but aren't. Otherwise, on disk, everything is the same. If I change things in two related libs, I have to commit twice, but I'm also changing two independent libs that I have to release separately anyway, just like in a monolithic repo. Finding and reusing code is independent of how many repos.

I just don't see any concrete problem in the article that I can relate to that explains how what we do is more work, causes problems, can be optmimized.