#1 is patently untrue; I go in there all the time via File > Reveal in Finder so that I can grab images to pull into other applications, mail clients etc.
Actually it is patently true - what you are doing is not supported, is not necessary and is dangerous - you should only access the photos using the supported methods
#2 - I thought maybe that was it too but it's on images both vertical as well as horizontal. There's even images in there that are just still frames of videos taken on iphone.
2 - the most common cause of un-expected "modified" versions is having the autorotate feature set on your camera - this causes a rotate flag to be set so that when yu import iPhoto does that and as always keeps the original and keeps the rotated version as mopdified
Given that you provided no information about your work flow one can only guess at common reasons
The jpeg preview of each video is also a modified version - as to why both vertical (portrait) and horizonal (Landscape) photos would have modified versions more information would be needed - the most likely cause is that you have made changes of some sort to them
LN