I feel any predictions on a timescale of millions of years is completely pointless. The assumption is always that you can just look at natural processes and assume that things will continue naturally.

Except we're already in the Anthropocene! The Earth no longer evolves naturally; it evolves according to our actions. And our abilities only increase with time. Even the position of the continents is something we can control if we want it badly enough. And eventually, as human capabilities increase, eventually even controlling the position of continents becomes a rather modest infrastructure project. It all depends on the scale and abilities of your civilization.

Hell, I don't even agree with predictions about the lifespan of the Sun. Stellar engineering is in principle possible, and we have many millions of years to figure it out. Really, it's not technically challenging; it's just a problem of scale.

So no. I don't think a supercontinent will form and wipe out humanity, unless we will such a thing to be so. And I'm not even assuming the future is all rosy. We could have a nuclear war, rebuild ourselves from the ashes, and repeat that until we burn through all the uranium, and we would STILL have millions of years to solve these very long term issues.