Look at this section, “User Accounts / What’s the difference between user and organization accounts?”
User accounts are intended for humans, but you can give one to a
robot, such as a continuous integration bot, if necessary.
In other words, a “User account” can be for a “person” (the normal case), but it can also be used by an automated process (a “bot”).
Which is precisely how Benbalter is using GitHub in the Change Agent project you cited above.
Q: How do I get one?
A: A “bot account” is just another Github user account. You create it exactly as you would any other Github user account.