On further reflection I'm gonna guess that the saucer was simply hot glued to the secondary hull. There are hints of SOMETHING under there (look forward of the shuttlecraft top piece in the aft view polaroid) but more likely it was simple bits to keep it intact for shooting. The builders, knowing the best angles for their design, wouldn't have finished every bit under it if it was not likely to be seen from that angle. They already knew where the mounting rod would be, so there was no way we would get a ventral-up look in the FX shot.
As for why the secondary hull was off-axis, well, it was obviously blown that way due to the two massive explosions in the Excelsiaucer and the secondary hull. Never stopped naval ships from sailing either.