I think what you are identifying as a CONTRADICTION is actually an EXCEPTION. The navigation here is little bit tricky.
The basic provision is laid out FIRST in 7.2.1. A box is preceded and followed by blank lines. Next in 7.2.1f Interior box lines do not have blank lines, BEFORE OR AFTER THE BOX LINE. Before of after the box line ONLY. It does not address blank lines before or after other text, but ONLY before or after the box line. This is consistent with 7.2.1c and d above that states that there is no blank line follwoing a top box line or preceding a bottom box line. This means that there is NEVER such a blank line for any reason. This point is emphasized by repeating it in the case of interior box lines that happen to follow right after the top box line or right before the bottom box line.
THEN, we journey over to 7.7 Boxes within Boxes, which makes quite clear that this is going to be about interior box lines. 7.7.1 itself states that boxes within boxes are [u]"transcribed in a different mannner than regular boxes."[/u] And THEN we get to 7.7.1c Insert a blank line before a top interior box line WHEN (and ONLY WHEN) it begins on any other line than immediately after the topy exerior border and d. covers the bottom interior box line in the same way. Look at the accompaying examples. The blank line is inserted ONLY when the interior box falls in between text that it in the box, away from the exterior box lines of the main box.
I found that looking at the examples helped me to understand this. Please let us know if you're still stuck.