I spoke with @nfagerlund and he pointed out that the docs are generated at https://github.com/puppetlabs/puppet-docs/blob/master/lib/puppet_docs/reference.rb#L69 which executes `puppet doc` with backticks, and per http://www.ruby-doc.org/core-2.0/Kernel.html#method-i-60 that only outputs to stdout. Logging warnings output to stderr, so this should be fine.