The paper can be found here: http://commonsenseatheism.com/wp-content/uploads/2013/05/Armstrong-Sandberg-Eternity-in-six-hours-intergalactic-spreading-of-intelligent-life-and-sharpening-the-Fermi-paradox.pdf
The main reason Dysonning the sun can be done at a fast pace is because of the exponential feedback loops. As long as we have some crude way of doing all the steps, then adding uploads allows us to automate the whole process, and get the exponential feedback.
If a process involves uploads, which are people, then it isn't "automated."
In a previous post (and the attendant paper and talks) I mentioned how easy it is to build a Dyson sphere around the sun (and start universal colonisation), given decent automation.
Decent automation includes, of course, the copyable uploads that form the basis of Robin Hanson's upload economics model. If uploads can gather vast new resources by Dysoning the sun using current or near future technology, this calls into question Robin's model that standard current economic assumptions can be extended to an uploads world.
And Dysoning the sun is just one way uploads could be completely transformative. There are certainly other ways, that we cannot yet begin to imagine, that uploads could radically transform human society in short order, making all our continuity assumptions and our current models moot. It would be worth investigating these ways, keeping in mind that we will likely miss some important ones.
Against this, though, is the general unforeseen friction argument. Uploads may be radically transformative, but probably on longer timescales than we'd expect.