I made Beta version 4.17.b2 available for download. Check “Beta version testing” section at the usual download page:
Short changes list could be found at readme.txt file.
In relation to problem you discovered – this version allows single site activated instances of URE to use its own copy of the settings.

The only limitation is automatic updates. This is possible from the Network Admin. In order to check if updates available URE should be active. But network Admin “Plugins” page shows active plugins for the main blog only.

Thus, if URE is not network activated and you plan to activate it individually for the subset of sites, you should activate it for the main blog in order automatic updates from the Network Admin will be available. In order input license code to the single site activated plugin use URE Settings under Network Admin – as explained above, this page is available in case URE is active for main blog.

Thanks for the help in testing.