1) Special Copy that this is either a symbolic link or a physical copy depending if your environment autorise or forbid the symbolic link.
So when Symbolic Links is allowed then Special Copy = Symbolic Link
When symbolic link is forbidden then Specail Copy = COPY
2) By default, JMS when a file or folder is not defined in the JMS template then it creates a Symbolic Link (or ignore it) depending that the Symbolic Link function is allowed (or forbiden).
Changing this behavior is dangerous in case where Joomla add new directories that was not defined in the JMS template.
In general, it is recommended that the master website is installed in a specific directory that is not public on internet. So that it is not modified all the times as you mention it.
Here, I suspect that the master is the www website and that you create slave site into a subdirectory.
3) If you want that the content of an extension is shared because it is not defined for the sharing, you have to send me the extension in the attachement of an email for review.
All the extension can NOT be shared.
To share an extension, it is required that this extension does not perform access to other data than the users. Otherwise this could create inconsistencies.
So a manual review of the code and all the MySQL queries is required to verify that there is no access outside.
See contact us for the email address
www.jms2win.com/en/contact-us