I recently learned this from BBC's Life in Colour documentary. It explained it, similar to the article (although the paper really dances around this hypothesis), that the flies had a hard time landing due to some visual weirdness from the stripes when the flies are close up. They had a lot of close-up footage of flies hovering above a zebra's skin but seemingly confused on how to land.
Intuitively, it does seem like stripes would make it more difficult to achieve focus for a compound eye, similar to how when looking through a chain-link fence or window screen it's easy to focus the wrong plane due to the spaced repetition.
Maybe the adaptation would require significantly more advanced visual processing with attendant increase in weight, size, and energy consumption, making it not worth it?