My interpretation of that (especially over a short period like this) is that sleep restriction causes swelling in the grey matter, which caffeine reverses. Interpreted like that, caffeine would be protecting the brain, not harming it.
Perhaps it serves an important protective or regulatory purpose which we haven't yet identified, because we still know so little about sleep and consciousness.
An analogy: There are lots of systems in your body that try to prevent and deter you from casually walking on a damaged leg, and we can override some of them with various external drugs, but that doesn't necessarily mean it's a good idea.
Maybe with chronic deprivation + caffeine habit, you're weakening your cognitive function - repeatedly using a misfiring neuron. At least, with no caffeine, you'd feel your memory is hazy and hard to recall, go to sleep.