I'll merely observe this - since I don't profess to know the answer. The IRS is well aware of the confusion and practitioner questions on this issue, which has now been going on for years. If they truly take the approach that mid-year amendments that do not contradict the specific terms in the Safe Harbor plan requirements under the regulation, then they could have just said so at any time and cleared up this mess once and for all.
Since they have thus far failed to do so, not even from the podium where it is unofficial - people are understandably concerned, and thus are often very (perhaps needlessly) conservative. It remains to be seen as to whether this conservatism is necessary or not. I confess that my modus operandi on such issues is generally that discretion is the better part of valor.
As to the question of whether the IRS, the qualified plan practitioner community, or both, are responsible for the confusion, I honestly have no informed opinion, nor, to me, does it truly matter at this point. Until the IRS issues guidance, I'll stick with conservatism. To a degree...and that's the problem with all of this - we all have to draw the line somewhere, and the line is often blurred.
It is astonishing that this one issue has caused so much trouble.