There should be no issues with using a subvar in a Make a Directory prompt value. If you are unfamiliar with RA FTP, it is best to play around with it by creating a test RA FTP Job and seeing what you can or can't do with it.
I was able to successfully create a remote directory using the following values:
Subvar is #folder=directory
Make Directory value is /home/qa4/user_tests/phm/test/{#folder}
The Job runs successfully and checking the remote server, the following directory exist:
/home/qa4/user_tests/phm/test/directory
One thing you note is that you can not make a directory in a directory that does not yet exist.
For example, you can not make the the following directory:
/home/qa4/user_tests/phm/test/directory/directory2
if the following does not yet exist:
/home/qa4/user_tests/phm/test/directory
In short, you can only create one directory with one Make Directory command .