Yes, saw that and downloaded the full report.
It appears this report used worst-case data for diesel and best-case data for gasoline.
The U.S. Energy Information Administration (EIA) referenced a European study which calculated that refining diesel fuel produced about half the GHG emissions that refining gasoline produced in European refineries in a 2009 report ("Light-Duty Diesel Vehicles: Market Issues and Potential Energy and Emissions Impacts"
http://www.tmaarc.org/Documents/LightDutyDiesel.pdf , page 26, last paragraph). It may be true that a very high demand for diesel fuel results in less efficiency per barrel of crude oil, but it seems unlikely it would result in that big a difference.
In U.S. refineries, the average "well-to-pump" GHG emissions from the production of ULSD fuel is 20,722 grams CO2e/mmBTU; 22,087 grams CO2e/mmBTU for E10 according to the latest version of the GREET model. The only reason it's even that close is that GREET assumes a lower "feedstock" GHG emission factor for E10 because of the ethanol in the fuel.
According to CARB's "Low Carbon Fuel Standard" Lookup Table, ULSD has a Carbon Intensity (CI) of 98.03 g CO2e/MJ, while Biodiesel ("Conversion of Midwest soybeans to biodiesel (fatty acid methyl esters -FAME")) has a CI of 83.25 g CO2e/MJ, and that includes 62 g CO2e/MJ for "Land Use or Other Indirect Effects". So T&E appears to be using some extreme ILUC factor to conclude that first-generation biodiesel is actually worse than ULSD in terms of GHG emissions.
Even then, T&E acknowledges in that report that renewable diesel from waste products like used cooking oil has GHG emissions that are nearly 90% lower than ULSD (Table 23 on page 43).