And ‘Yes’ I should re-test what is happend now with network wide settings from the ‘Multisite’ tab. It may stop working.

After thinking a little I went to the conclusion that there is no problem here. If plugin activated for single site, all plugin’s settings should be applied to that single site only. So if it is needed to restrict single site administrator, super admin will set needed options at the “Multisite” tab at this site. Single site admin will not see the “Multisite” tab of URE.