Hi, Ben – my apologies in advance if I don’t understand your question correctly, but the way you have asked it isn’t the way that WordPress multisite works. A multisite network is either in subdirectory mode or subdomain mode. It isn’t possible to have both types of sites in a WordPress multisite installation. Therefore, the Cloner can only create new clone sites in one or the other mode depending on the type of WP network it is used in. It also cannot clone individual pages. But the only way to put a “page” in a different “Directory” is to make it a sub page of another page in which case the parent page becomes it’s parent “directory” in the URL.
The Cloner copies entire sites (including pages) but only to the type of site of the network it is already in (subdomain or subdirectory). Hopefully this helps.
All the best.
