After some research and tinkering I'll answer my own question :
First, the [FeatureSettings] section was reordered inside the "Kobo eReader.conf " so that it was in the middle of the file instead of at the end but still present.
Second, the option works only for folders beginning with a dot located at the root of the kobo as displayed when plugged in a computer. In another word, a dot folder located inside another "regular" folder will not be ignored and its files will be loaded in the library.
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