When I spotted and reported them it was on v5.0.2800. (5.0 SP1)
The hotfix (v5.0.2860) only fixed the ecommerce payment details issues, they haven't changed the project configuration since.
Both files are physically there, just not included in the project/solution (opposed to your two files who are still included but no longer exist). Since they aren't part of the solution, they won't get published.