Looking at the FileZilla source code:
- https://svn.filezilla-project.org/filezilla/FileZilla3/trunk/src/interface/QueueView.cpp?revision=10972&view=markup&sortby=file#l1898
- https://svn.filezilla-project.org/filezilla/FileZilla3/trunk/src/interface/QueueView.cpp?revision=10972&view=markup&sortby=file#l2731
... it does not look like it supports any kind of mechanism to inject any information at all into the command.
The command is executed exactly as entered.
After all is command run "after queue completion", not after particular queue item is completed. And the queue as a whole is not related to any particular file or folder.