First, props for continued development on your plugin.
I have a suggestion for handling activation on a WP network. I think if the plugin is network activated, then the settings for the plugin should appear on the network settings menu, not on the settings menu for each site. This would enable network-wide management of the plugin. In a perfectly customizable world, there could be a configuration option when the plugin is network activated to also give site admins the ability to customize/override the network settings, where those settings would appear on the site settings menu, but I'd have this turned off by default. However, if that configuration option didn't exist, then there would be no settings on the site admin menus and use of your plugin when network activated would be limited to super admins.
In my experience, most WP network operators opt for network-wide activation when they want centralized management of options. In most instances, if a plugin is network activated, they don't want settings on the site admin menu.
A lot of security plugins (such as the login limiters you mention) follow your approach to settings, and I think that's less than ideal and makes adoption/management on a network harder.