Yes, we don't know how to make a half-ton replicating probe right now.
No, none of the arguments on the article have any implication on the possibility of such a probe. None at all.
There's something to look into at the durability argument. The article has no usable information on it, and it's probably not a showstopper. But again, the only thing on the article is that yes, we don't know how to make one such probe right now.
The self-replication assumes also that there is enough energy stored in each planet (or coming from a Sun) to do the work... That is pretty much unlikely.
I hate this assumption that many sci-fi enthusiasts seem to make, that as long as something is not ruled out by currently known physics rules, it doesn't matter that we have no idea how it could be built, there will be some way in some plausible future.
When we see currently insurmountable problems in creating a piece of technology, it's absolutely possible that we'll never be able to build it. Even if it is theoretically constructible, there is no reason to believe that the way to build it would be found before, say, the sun runs out of hydrogen.
I would also think that self-replicating probes would work more like living things. He seems to be imagining that we make probes like modern machines, and then find ways to let them build themselves. But nature found much easier solutions.