This is awesome, thank you a lot for the write up and sharing your experience!
First of all I want to thank you for noticing all the little stuff about the case and the packaging, it really wasn't simple to design and I wasted countless hours to make everything fit and align 
You also noticed some interesting stuff, like the picture of the screw missing from the MBO part of the manual (silly error on my part but you assumed well) and that longer screw (included that one for the right panel near the PSU side, if the short one is not enough).
Regarding the riser yeah the bracket was designed for the reverse cable entry, yours has the cable coming from the bottom of the PCB but I am glad if it all fit in the end, doesn't matter if the bracket flexed a bit.
Also about the power connector, it is somewhat expected with itx boards. You can either offset the whole connector a bit with a standoff, or get a pigtail adapter from our shop, it will look something like this once installed:
