I agree that they can be prospectively eliminated if they have not yet entered the plan, I'm not sure if that's what EOB is referring to there. My copy of the EOB is in dead tree form and sitting in an office which I don't expect to return to any time soon, so I can't reference it, but I am not aware of any superseding guidance. The plain language of 2016-16 pretty clearly prohibits any "mid-year change to reduce the number or otherwise narrow the group of employees eligible to receive safe harbor contributions."
I can see an argument in favor of allowing it though. Since a SH plan is not required to provide the SH to HCEs, you could structure a plan to provide that the SH is given to NHCEs and a separate, 100% vested match with the same formula is given to the HCEs. There would be no functional difference between this and a safe harbor plan that covered all employees, except that the match for the HCEs could be eliminated mid year. If you can do that, why shouldn't the option be available to all SH plans without the extra complexity?