There are 3 gems vendored in both puppet-agent and pe-r10k:
Currently the packages do not conflict, but only because:
minitar and ffi are vendored only on windows for the agent and only several linux OSes for pe-r10k
the vendored versions of semantic_puppet are different between r10k and agent
This is not good, considering if r10k were ever to supply a windows package, or r10k updated the version of semantic_puppet, the packages would actually conflict.
However, the fix may not be as simple as removing the gems from r10k, as there are reasons we do not vendor things on specific platforms. We need to investigate this in detail before ripping out any gems or vendoring gems for all platforms.