We have a couple of fixes and small improvements for you in PyCharm 2017.3.1, if you'd like to already try them, you can now get the release candidate from the confluence page.
New in this version:
Several issues with running Python modules (-m) were resolved: running modules remotely, showing command line after running
Further issues with running code over SSH were resolved: they can now connect to IPv6 hosts from macOS, don't misinterpret `ProxyCommand: none`, and correctly parse the `HostKeyAlgorithms` option (Connecting to a Python interpreter over SSH is only supported in PyCharm