Hello
from the manual p.16
http://www.agisoft.com/pdf/photoscan-pro_1_3_en.pdf"In the Generic preselection mode the overlapping pairs of photos are selected by matching photos using lower accuracy setting first.
In the Reference preselection mode the overlapping pairs of photos are selected based on the measured camera locations (if present). "
It answers the question "where am I supposed to look for matches?do I match every single image with all the rest?do I use reference coords to figure out which images might overlap?"
The guy in the video is using an older version where he could only choose one or the other.
I don't think that the "re-read data from the UAV images" is entirely accurate.
If you import approximate reference coords and leave them Checked, they will be taken into account during the alignment process.
If you Uncheck them and use the reference preselection, the images will be matched faster and will not affect the alignment.
Judging from his latest comment on the Youtube video to another guy that points that out, I suppose that he misunderstood that part.
I hope this helps and please correct me if I am wrong.