1) If you want that we create a specific plugin that does not share the shopper table, we can do that with our billable support that you can order at
www.jms2win.com/en/joomla-multisite?page...35&category_id=1
This can be done at your own risk as this may have inconsistent data present in the DB.
In general, 1 hour of billable support is enought to create such specific plugin to add a specific sharing definition for you.
2) Changing the logo can be done by several method and depends how it is managed by the joomla template. We don't know how S5 manage the logo.
When this is in a CSS, you can modify the CSS to make reference to a specific /images_specific folder or any other specific directory where you would get the logo.
If the logo is a parameter in the back-end of the template, change the logo path or reference in the back-end.
If this is a module that display the logo, you can also update the module definition to specify a specific location.
You can also use the Search/Replace plugin to search for a "generic logo" file and replace it with a specific website dependent logo.