So the reason why the upgrade isn't happening is because cmd_exec on a osx/x64/shell_reverse_tcp session does nothing currently. For some reason these sessions are being reported as session.type basic:
Which means:
https://github.com/rapid7/metasploit-framework/blob/master/lib/msf/core/post/common.rb#L84
doesn't invoke session.shell_command_token.
I can fix this either by adding an else or when 'basic' clause to the case, e.g:
timwr@57e8454
or by ensuring that session.type is set to shell?

I think #10448 had a merge conflict, and the def type function was removed, (not to be confused with the def self.type function )
Putting it back seems to fix the issue:

msf5 exploit(multi/handler) > sessions

Active sessions
===============

  Id  Name  Type           Information  Connection
  --  ----  ----           -----------  ----------
  1         shell x64/osx               ...

Without the fix:

msf5 exploit(multi/handler) > sessions

Active sessions
===============

  Id  Name  Type           Information  Connection
  --  ----  ----           -----------  ----------
  1         basic x64/osx               ...

Looks good, thanks @timwr

Release Notes

OS X command shells now have their session type set correctly to enable upgrading to native Meterpreter.