That is an interesting question. The spacecraft is not in earth orbit, but in a trailing solar orbit. But still, the orientation would need to be as you describe for it (an exoplanet) to obscure the view irrespective of the spacecraft's orbit relative to earth.
Wiki's article on Kepler says that the observed star systems are the ones that are on a similar galactic plane as ours - maybe that makes a difference - same plane, same orientation? I don't know. Where's Neil deGrasse Tyson when you need him?
Checked your Kepler Wiki page which leads to this page:
http://jwleaf.org/docs/probability-of-planetary-transit.html
Those scientist-types think of everything. :-)