No? They're talking about something mostly orthogonal to the joke, which is whether it actually deserves to be in the list.
It's the difference between "here's three very hard things, let's make a joke with them" and "here's two very hard things, but we can make a joke if we shoehorn in a less-hard thing".
I always assumed that at the time it was a relatively harder problem, with lower-level languages that are mostly array-focused, no real built-in containers and no for-each support. This was cured with better programming languages.
On the other hand, cache invalidation and naming things are problems that grow harder and harder when systems get more complex, which they obviously did.