Bren is probaly right. Attached to this post is an analysis of the lines on the station (picture from a few seconds before Bones' screenshot), extrapolated out to see if they match. The red lines (the docking enterace) meet at completely different location (off screen) to the green lines (points of referance from the dome's slant).
However, analysis of both sets the scematics shows that the slant of the dock enterance and the Dome's slant are equal, meeting at the same point off the image. At this point, I may have to side with the easier option of letting the current model stand as it is - because modeling it to by square with the ship could prove difficult - and would require a redesign of the outer and inner sections of the enterance.
I'm willing to attemt it though, if enough people want to have the docking enterance changed - it's not too late to make adjustments. If you'd like it edited, please say.