I spent some time figuring out the differences between 4:3 and 16:9 photos. These are my findings with respect to the exif properties,
For 16:9 photos
Property ‘Orientation’ not present
Property ‘Rotation’ is always 0.
Image size reflects rotation, e.g. 4032x2268 for landscape or 2268x4032 for portrait
For 4:3 photos
Property ‘Orientation’ present, and correct, e.g. ‘Rotate 90 CW’
Property ‘Rotation’ present, and correct, e.g. ‘270’
Image size is always 4032x3024
Possible explanation
To me this seems to indicate that PhotoStructure does not apply rotation at all.
For 16:9 photos it just so happens that the iPhone encodes the picture “as it should be” already, so not applying a rotation gives the correct result.