Hi! This can [for the most part] only be set when you install WP multi-site for the first time. When you convert WP to multi-site mode from a regular install you have to chose at that point whether it will be a subsite network (site.domain.com) or a subdirectory network (domain.com/site).
The screenshots were taken with the cloner running on a subsite network. But the cloner automatically detects what type of network it is running on and presents the correct interface. If it is showing what you describe it means that your WP multi-site network was configured as a subdirectory network. There are ways to change it after the fact, but they are very NOT recommended unless you really know what you’re doing and know how to navigate all the potential ways to hose it up pretty badly.
Depending on how “live” your WP network is, you either have to re-install wordpress and set it up as a subsite network or google how to switch the type of network over (again highly NOT recommended). Those are really the only options for what it sounds like you want to accomplish.
