From the looks of it, I may have some work ahead of me for a new update.
First thing is a permissions issue when it comes to multisite: https://codex.www.ads-software.com/Roles_and_Capabilities#Additional_Admin_Capabilities.
In multisite, only the super admins have the ability to to create/edit/delete users. This makes sense and is a design decision made by the WP core developers.
For that reason, I believe the code around https://plugins.trac.www.ads-software.com/browser/bp-registration-options/trunk/includes/admin.php#L265 was implemented. I’m having trouble remembering at the moment if it was me specifically, or if that’s code that was there when I took over as lead dev, that I’ve since tweaked. Regardless, it’s there, and it’s preventing the menu from showing up on more than the main site, out of the box. I’m pretty certain the filters were added by me, being forward thinking, because I would like to make it so that for the duration of using our plugin’s code, sub-site administrators can moderate incoming potential users, but nowhere else.
However, and this is where my work ahead of me comes in. While I was troubleshooting and trying to recreate what you’re describing, I came to realize that my 4.2.0 release is not working on multisite at all. This is, I believe, my likely leak that I wasn’t managing to figure out, when I had people still reporting that people were slipping through.
Regrettably, that doesn’t likely give a workable solution to your initial question/issue. You can tinker around with those two filters and see if something ends up being workable for you, or if you are adventurous, comment out that primary if statement check and see if you reach a workable solution with those as well. Let me know if you do find something, and I’d gladly take contributions/pull requests on github and give proper credit.