I have a internal routing cable kit but found it much easier to route the cables with a brake cable following the techniques from this youtube video

1. Yes. It rotates so cannot be perfectly flush with headtube
2. The stem should have small indentations where those pins go. Make sure you align the stem exactly so indentations match with pins on spacers.
3. Yes. I am not a fan of that VB cap. You can't have those fancy caps on Ali express fit on it.

I had a hard time getting the pins to align with the holes in the integrated handlebar when I put the spacers and front fork together on the frame.  The hole and pins were just off by a little bit and would not seat together.  I enlarged the holes on the integrated handlebar so that the pins can seat inside the holes.  Luckily I had a very small drill bit that probably increase the size of the hole by half a millimeter.

The top cap that came with the integrated handlebar did not fit nicely.  I decided to just use the top cap from the compression plug.

I want to get this frame but I am not certain which size would best fit me (49cm or 52cm).  I'm 5'4.5 with a 29" inseam, 50 years old.  I am currently riding a Trek Emonda 2015 52cm with a 80cm stem.  I am leaning to towards the 49cm frame since the offset in the seatpost would add to the effective top tube length and reach.  My concerns about the 49cm frame is the low stack.  I'm not sure if my 50 year old back can handle such a low stack.