Multiple problems with Multisite install

I’m using this plugin with a Multisite install and am activating it only a site by site basis. I’ve never done a Network Activate yet this plugin affects ALL sites whether you want it to or not.

An entry is added to the multisite admin panel that lists all sites, whether or not the plugin has been activated for that site. Why do you do this when Network Activation hasn’t been specified?

Multiple tables are created in the database that do not start with the randomized specified in wp-config. These tables are skipped by my backup plugin. Why did you do this?

As mentioned in another thread, removing data from one site removes data from all sites. Why?

In my opinion much of the above works contrary to how WordPress intends plugins to function in a multisite environment. As a result I’ve disabled the plugin and am looking for an alternative.