This is precisely one of the areas in which Git shines. It used to be a pain to maintain your own patches on top of an open source project. But with Git it's easy.
Git helps with keeping track of your patches, and can deal with simple structural changes, like if a function you've modified is in a different position in the file. But it's still up to you to deal with real functional changes coming from upstream, and I think that's the author's main point.