Desktop/AppData/Icon files are installed in a wrong place during make install

I have noticed this when trying to update the Armagetron Advanced Flatpak:

 /usr/bin/mkdir -p '/app/share/armagetronad/desktop'
 /usr/bin/mkdir -p '/app/share/armagetronad/desktop/icons/48x48'
 /usr/bin/install -c -m 644  icons/48x48/armagetronad.png '/app/share/armagetronad/desktop/icons/48x48'
 /usr/bin/install -c -m 644  armagetronad.desktop armagetronad.appdata.xml '/app/share/armagetronad/desktop/.'
 /usr/bin/mkdir -p '/app/share/armagetronad/desktop/icons/16x16'
 /usr/bin/install -c -m 644  icons/16x16/armagetronad.png '/app/share/armagetronad/desktop/icons/16x16'
 /usr/bin/mkdir -p '/app/share/armagetronad/desktop/icons/32x32'
 /usr/bin/install -c -m 644  icons/32x32/armagetronad.png '/app/share/armagetronad/desktop/icons/32x32'

I am not sure what is going on. The correct locations should be /app/share/applications (for desktop file), /app/share/appdata (for AppData file), /app/share/icons/hicolor/48x48/apps (for 48x48 icon) etc.