One answer that has occurred to me, and I think deserves knocking down quickly, is that the possibility of overflying the worst might have seemed a 'least worst option'
Another, that whilst potentially safer lower down as far as maneouvre margins are concerned (& thus actual 'upset'), roughness of ride and high airframe loads can likely be more guaranteed and last longer (transit time)
Both are possibilities. That is why it is imperative to AVOID these areas.