It is normal that you have "multi sites" present in the slave site as you have asked to replicate the master website in which it is present.
As you clone the master, you receive a copy of it.
Yes this is a configuration that is correct if you want to replicate the master website.
If you want to create a fresh slave site without anything, you have to let the "template site" empty.
In this case, you will have an empty joomla without anything pre-installed.
If you want to have copy of the "/images", "/templates" directory, ..., you have to change the "special copy" into copy in the "template / file and folders" tab.
See tutorial video CP-05.
www.jms2win.com/en/tutorial#jms12x-CP-05