I’d actually cut the knot, not just hold it below, and weave in the ends on the machine.

I expected one of the tips you had mentioned in a comment some time ago. Using a ball winder will most likely reveal knots that might become problematic later.

I've mostly embraced the knot, otherwise I do what you did.

Most of the time I'm working from cakes rewound from skeins or hanks so I will join them (outside end of one cake to inside end of next cake, etc.) with a Russian Join before hand. Other times if I haven't pre-joined them I'll see the end well in advance and will make the call to join a new cake at the end of the present row even if I have a foot or more of yarn left. I can always cut off long tails to use for sewing up seams!