@rowdenw Found it! I found the bug. Profiling and debugging changes to app extensions is trickier than one might expect, and that’s my excuse for why this took so long to find, because it’s specifically my fault. 
The fix for this will be in the next version of Codebook for macOS, 4.5.3 (4.5.2 was released earlier today). For anybody looking for a work-around in the mean-time: disable the anonymous statistics preference in the Codebook for macOS Preferences window.