Having synchronized folder directly in APPDIR and setting subdir on first level as "do not overwrite existing files" will result in creating root synchronized folder even if feature not selected for install.
How to reproduce
Create 2 features and and 2 syncronized folders directly in APPDIR. There should be one folder inside this synced dir and we set it to "do not overwrite existing files". Set each folder to own feature. When installing only one feature empty folder of other feature is created. This only happens in case structure is:
APPDIR/Component1(synced)/config(do not overwrite) => Feature1
APPDIR/Component2(synced)/config(do not overwrite) => Feature2
When Only one Feature is selected for install (for example Feature1) end folder structure is:
APPDIR/Component1/config
APPDIR/Component2(empty)