Thanks guys — I was afraid it was something like that. I absolutely hate it when Mac software litters stuff outside of its bundle without even asking the user. Plenty of people figured it out correctly — GitHub.app, for example, installs a copy of the git command-line tools into its ./Content/Resources/git, and remains self-contained and clean.

GPGTools guys — if you're reading this thread, please please stop installing stuff outside your plugin's bundles.