If you download all files as zip from an agent workspace folder, it doesn't contain the parent folder.

If you download all files from archived artifacts or master workspaces it does contain the parent folder.

i.e.

http://server/job/project/ws/dirA/*zip*/dirA.zip

content of dirA.zip: 

./file1

./file2

./folderA/

-> does not contain parent folder dirA.

http://server/job/project/lastSuccessfulBuild/artifact/dirA/*zip*/dirA.zip

content of dirA.zip: 

./dirA/file1

./dirA/file2

./fdirA/folderA/

-> does contain parent folder dirA.