Ok I understand now.
BPS is not a typical plugin and .htaccess files have certain requirements that will only work when used in the Primary Network/Multisite site at this point. It is of course possible to make BPS work from the Network Admin panel, but this feature request development is currently not scheduled. I will add it to the BPS development schedule. This could take a very long time to be created (months). Before any new feature request is considered there is a lot of research and testing that is required before development will start.
A simpler approach may be to add a new feature/option/setting that you can choose which Super Admins are allowed to see the BPS plugin menus and pages.
Example Option Setting:
Allow ONLY These Super Admins to see BPS menus and pages:
Enter the Super Admin User Id’s here that are allowed to see BPS menus and pages: 1, 2, 3, etc.