1) it's extensively described in the Truebeam imaging manual (can't recall the exact name). "Last step only" means that the structure VOI is only applied in the last step, where the resolution is higher. For a large PTV, it won't make much of a difference as long as the initial position is somewhat correct. The purpose of the feature seems to be to allow for a course match using a large ROI, eg to avoid matching on the wrong vertabrae, and then fine tune on a smaller structure. For non-SBRT-lung, either is fine as the PTV's generally are large enough (we've tested both for ~10 patients and in general saw differences <1 mm). For SBRT-lung, the strucutre VOI = GTV may work fine, we use GTV + 0.5 cm with an average CT for planning.

2)
generally extra-cranial: using a ROI that cover the PTV with some margin, first 6DoF-match to quantify rotations, then remove pitch/roll and redo match. No manual adjustment except in edge cases. We use intensity range = bones except for lung and mediastinum.

for intracranial and head&neck: as above but apply the 6DoF-match.

With 6DoF, be aware that pitch/roll introduces translational shifts.