What happened 100 to 200,000 years ago?
Selection pressure caused by environmental changes. Evolution never stops. Many of today's species are sufficiently different from their ancestors to be designated as new species within the last 100,000 - 200,000 years. That's all.
I wonder if the "species have very clear genetic boundaries, and there's nothing much in between" is a finding that still supports as you said species being the tips of branches or not
Yes that's exactly what it means.