While @orthocresol was busy finding the Carreira paper, I was busy constructing my own thoughts on the stereochemical consequences of the reactions of 1 (iii) and 5 (ii). Yes, it is an issue of conformation. It is far easier to rationalize the results after the fact. To predict the most reactive conformation of epoxide 1 the Newman projection 2, viewed along the red bond of 1, places the two carbon chains anti to one another. Intermediate 3 undergoes straightforward SN2 displacement at the allylic site.
In the case of epoxide 5 (ii), the two alkyl chains maintain the anti positions in conformation 6 but now the carbon-bound chlorine acts as a neighboring group in an intramolecular SN2 displacement to form intermediate 7. This species suffers a second SN2 displacement to afford 8 with retention of stereochemistry at the reacting site. Compound (i) follows the same pathway as 1 (iii). The role of water is to cleave the silylether.