In the first countries where Omicron spread, such as South Africa, it was first detected in young people where vaccination was very low. And just like Delta or Alpha it started to diverge before mass vaccination was a thing. The article you linked even suggests Omicron may have developed in mice, which are obviously not vaccinated, so the mutations would not be driven by selective pressure against vaccination.

Evading vaccination could very well be why it was so fast to spread in mostly-vaccinated populations in Europe and North America, which happened "faster than any previous versions" as the (very interesting!) article you linked says at the very beginning, but the variant was more fit anyway.