Good question, and I would say the difference is in a subtle but significant effect. A comma is a pause represented by a single punctuation point. And it represents a complete, temporary pause. An ellipse on the other hand, at least to me, illicits a feeling of hesitation or tapering off. This is because instead of stopping suddenly, an elipse extends itself, its composed of multiple periods. For instance a comma is like turning a switch off, then on again. And an ellipse is like stopping a car, and then starting it again. It doesn't stop instantly but takes a couple of seconds to fight the momentum. And then you have to start it up again. Therefore there is something certain and almost forceful about a comma, but indecisive or vague about an ellipse. So if you want to convey an ambiguous pause, I feel like an ellipse is better suited.
I suppose a specific example would be like this. If I wrote "hmm...", at least in my head I would continue pronouncing the lingering "mm" sound. To the point that if I wanted to technically convey how I pronounce "hmm..." without the ellipse, I would have to spell it it as "hmmmmmm". The ellipse is like hitting the break button, I don't pause immediately. But if I read "hmm," I literally stop my pronunciation after the second "m". Like a binary system of on and off, once I see that comma I fully stop, pause, and then continue.
This is how I distinguish the two, but I could just be weird lol