Yes, and apparently longstanding one: Plugin tickbox not getting enabled · Issue #3 · pkp/shibboleth · GitHub
I don’t think so. I only see references to plugin settings in the Handler.
Alec bumped this to a 1.0 release in master, but we probably don’t want to package it as a 1.0 release until the above bug is fixed.
Yes, this plugin is “all or nothing” currently.