Update pup acceptance tests to use the CA CLI to generate certs

Currently, puppetserver generates its CA files on startup. Before we can remove this behavior in favor of require people to run the CA CLI tool to set it up, we need to update our tests to use it, so that things won't break when we actually remove the bootstrapping.

This will most likely be an update to the install utility methods in beaker-puppet, though it might implicate some individual tests as well. Tests using utilities from beaker-pe might also be impacted unless they use the PE installer, which will be separately updated to use this tool (see PE-24739).