It seems like the nightly repos configured in pre suite step 15 of the acceptance tests might be getting overridden in a later step by beaker. Commenting out step 15 doesn't cause the tests to fail to install puppetserver/agent. Step 20 calls install_puppet_agent_on a method in beaker-puppet which looks like it installs the release repos.
Figure out if the nightly repos are ever actually used and update the tests to use them when NIGHTLY=true.