I don't really know why they use the term "safe harbor" in 1026.35(c)(3(ii)--to me, the bottom line of what it's saying is: Do things this way to comply with the HPML appraisal rules. Period.
Here's a scenario: You do everything just like it says in 1026.35(c)(3)(ii)(A) - (D). However, it turns out that the appraiser you had perform the appraisal had lost his license. Or it turns out that in this particular instance, because he had recently been in the house, he cut a corner and did not go in the house for this inspection. Without the safe harbor language, you'd technically be in violation of the regulatory requirement to have an appraisal conducted by a certified or licensed appraiser who conducts a physical visit of the interior of the property that will secure the transaction. But the safe harbor language gives you protection from that technical violation because you did those things.