Why is Kyoko not present in Madoka Magica's official artwork?
There are many other official artwork for the series. That is the cover of the DVD box set and like you said, the other image where Kyoko is not included is the cover for the first volume of the manga. 



This is probably also the reason why Netflix used that artwork as its listing.

I think iconic is subjective in this case. Someone more familiar with the movies will think differently, as you'll see later, but there are a lot of other official artwork where only two magical girls are featured at a time:



I do think that the reason why she's not included in that artwork is because she's not involved in the first three episodes (there's 12 episodes and the set contains 3 discs, assuming the first disc only contains the first three episodes). At least Sayaka is introduced in the first episode, which is presumably the first episode the viewer will watch after purchasing the discs set. Bear in mind that the cover for the discs set differs from region to region. 

Finally, the artwork for the disc for the first movie, as well as the movie posters, includes all of the magical girls:



In the first movie all of the five characters are introduced and played significant roles. So this theory is not that far-fetched.