Will upgrading to Redactor 3 keep my configuration from Redactor 2?

Most of it, yes. The Redactor 3 upgrade will automatically create a configuration set based on your Redactor 2 system settings. That will keep most of your configuration in tact, although you should anticipate that some things don't work exactly the same between v2 and v3, so we recommend inspecting the set and making sure the configuration matches what you'd expect.

The upgrade does not cover context overrides, or overrides from the custom template variable. Those will need to be manually applied again after the upgrade.