The build process currently includes $(DESTDIR) outside of the install and uninstall targets. This runs into issues when using $(DESTDIR) to install to a different location than
/: The aerc program and its configuration files expect the folder structure under $(DESTDIR) to be present on the target machine, which is wrong according to the GNU documentation for $(DESTDIR) 1.
This bug was found when packaging 0.3.0 for Debian 2. I've got an idea how to fix it and upload a patch once its finalized.
This bug impacts at least aerc 0.3.0 and 0.4.0.