Firstly regarding the message, somehow warn that it will delete roles if not set in the main site. At this stage it says it will copy over the roles but doesn’t indicate if there is a role in the subsite that is not under the main site, that it will be removed.
I understand it would be a very difficult thing to do and not everyone would want to do it.
I personally would be happy with maybe an option to manage roles globally as I described. In terms of different roles for a user on different sites. The user role is not set globally, so I should be able to access all roles for all sites in one place and sync all sites to have same roles. Not sure how that will work for capabilities thou as WooCommerce capabilities wouldn’t be in a site that doesn’t run it (maybe auto add them). Then each user would be set a particular role per site, ie. they might have Admin for a subsite but only subscriber for the other sites.
I imagine (and am open to suggestion as I am not a WordPress developer), that I could open a list of all roles globally, which when I go to edit that role, it collects all capabilities available globally. Once I set it up to my needs, I could then apply globally. If I need to adjust a single user I should edit that users roles and capabilities. I don’t expect to be able to have the same role on 2 sites each with different capabilities. More of just a way to be able to manage all roles on a global scale rather than each site.