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.