These are two editions that were assembled at different time periods. Editorial practice changes through time, and is sometimes privy to the prevailing academic fashion of the time. Even considering the most urtext of urtext procedures, we are still dealing with an interpretation of an editor or editorial board to the primary sources at hand. In many cases the creator is not available to set the record straight, so to speak.
IMO, the score can be at times blatantly insufficient in its ability to lay out what the true intention of the composer was. All too often, scores are interpreted under the guise of a one-dimentional, all-encompassing, and absolute definition of what is perceived to be a static state of being. A single unquestionable truth. Many performers that have worked with living composers can attest to the continual evolutionary nature of a composition, even after it has reached its final performance-ready version.
A scenario to think about:
Should we be reading Bach's keyboard works in C clefs as he wrote them? The music certainly looks more elegant in its original clefs, centered on the staff with fewer ledger lines. But is this the best choice for modern eyes schooled in the procedures of modern notational conventions? Is the musical idea changed by writing everything out in either a treble or bass clef?
Nonetheless, when the successor to the Ekier edition is assembled, perhaps there would be those in the future that question the editorial practices of the Ekier edition which today appear to be sound judgement.
If one wants a clearer framework upon which to interpret a given score, a wise course of action would be to examine multiple editions of a given piece and not to rely on a single publication for "absolute authenticity."