The article states that 'his genetic affinity is similar to the ancestry appearing in Anatolia and the Levant during the Neolithic and Bronze Age.' As a layperson, I don't think we would find this particularly shocking. It's well known from written sources that there was significant communication and movement between Egypt and those areas during the broader Bronze Age, even extending back into the Neolithic for some cultural exchanges. This even aligns with biblical narratives that describe individuals and families traveling to and from Egypt for periods of time.
Worth noting for context that "Anatolia and the Levant" (better known perhaps as the Ancient Near East) also included plenty of darker-skinned folks in that time period, with an appearance that we might nowadays associate with Sub-Saharan Africa - and they were highly integrated in their societies, not just a servile underclass. This is also true of the ancient Mediterranean region as a whole. We're especially sure about this because of surviving pictorial/visual (e.g. from the Minoan civilization in Crete) and textual sources. So our Old-Kingdom Ancient Egyptian could well have looked quite "Sub-Saharan" in appearance, despite not originating anywhere south of present-day Sahara.