How do the known abrupt climate change events fit into the xkcd Earth temperature timeline?
The apparent contradiction comes primarily from #1 but #2 also pays a small role here...

Temperature decreases during the Younger Dryas greater than $2^{\circ}$C are believed to have occurred almost exclusively above $30^{\circ}$N in latitude. The bulk of the tropics are thought to have been relatively stable during this time and the southern polar region showed slight warming. Additionally, global temperature averages are generally weighted by area and only one fourth of the earths surface lies between $30^{\circ}$N and the North Pole. All this combines to produce what is thought to be around 0.6$^{\circ}$C of global cooling at the start of the Younger Dryas (Carlson, 2013).

Randall does cite several sources in the top right of his graphic but Shakun et al. (2012) is the only one that presents meaningful temperature data during the Younger Dryas. And in fact, the comic's proxy data (dashed) temperature curve closely matches the temperature curve presented in this article over this period (curve d in the figure below).



Interestingly, while Shakun et al. (2012) does show a global temperature decrease close to $0.6^{\circ}$C 12,000 years ago, the change doesn't appear to happen abruptly (at least not on the scale of decades). In the text of the paper the authors state that they built their temperature data set from 80 different proxy measurements taken over a wide range of locations. It turns out that these proxy measurements have a relatively long time resolution (a median value of about 200 years). That means that while the changes may have occurred very quickly this temperature curve is going to fail to capture that variability and appear "smoothed out". This does make the xkcd graphic a little misleading since the large temperature increase at the end is produced from data using a much finer time resolution, but this is a flaw common to all "hockey stick" temperature plots.