Hi - thank you for the clarifications.
Some have reported issues running the Cloner with multisite installed in a subdirectory and running in subdirectory mode. We haven't really been able to reproduce all the problems ourselves, but have made some fixes to support this. It should work in that setup. Sometimes issues with permalinks or .htaccess cause problems with this configuration. Generally, we don't recommend running multisite installed in a subdirectory. Our opinion is that it's better to always run multisite under a top level domain even if it means getting a different domain to host it. Things are much more straight forward when the root of a multisite network is installed at the root of a domain. But everyone has different needs.
In terms of the best workflow for translated versions of sites: the Cloner does not maintain any kind of link between a clone and it's original site. Once the operation is complete, the new subsite is a completely independent set of the content. To provide an accurate answer I looked at how MSLS works and stores its data for post linking. It stores those in the wp_##_options table(s) per site. Knowing that, this would be my recommendation for workflow:
1) install / start with a blank network
2) build your initial "home" language template site - this will be the site you clone. Do not install, activate, or configure the MSLS plugin on it yet. For example this might be mysite.com/en with all content in English and the Language set to English in Settings > General. Get it exactly the way you want it with all plugins / theme / content / etc.
3) clone mysite.com/en to mysite.com/es (both will be in english at this point and /es will be a copy of /en.
4) change the language setting for /es.
5) install the MSLS plugin and configure the settings separately on both /en and /es... add the widget to each site, etc.
6) edit every post on /es individually and:
a. update the content to the translated content
b. use MSLS to map it to its translated equivalent post on /en
You can also clone sites after doing all that, but what will happen is that you will get a duplicate site for a particular language. That is ok, but you will still have to repeat steps 4-6 for any site cloned with MSLS active.
Also take note: even if you deactivate MSLS the configurations it makes (the post mappings and its settings) are still in the database and will still get copied in a clone. If you then activate the MSLS plugin on the clone everything from it's origin site will be there too.
The best way to get a feel for all this is to play with it and experiment for yourself.