Add vault timeout flags + var_source GC interval

[aoldershaw]

Why do we need this PR?

New flags added in concourse/concourse#6362

Contributor Checklist

• [ ] Variables are documented in the README.md
• [x] Which branch are you merging into?
  • master is for changes related to the current release of the concourse/concourse:latest image and should be good to publish immediately
  • dev is for changes related to the next release of Concourse (aka unpublished code on master in concourse/concourse)

Reviewer Checklist

This section is intended for the core maintainers only, to track review progress. Please do not fill out this section.

• [ ] Code reviewed
• [ ] Topgun tests run
• [ ] Back-port if needed
• [ ] Is the correct branch targeted? (master or dev)