Why do I shake hands with somebody I don't like?

Assuming a certain setting - yeah we tend to autopilot. Go through the motions.

Years ago I was working at a store, I had a heated argument with some customer, but then after it was all over I said, "Okay thanks" like I would any customer.

He left and I thought, "what the h3ll just happened?"

I prefer Namaste 🙏, or just nodding my head with a polite Hello.

I don't. ☺

You answered your question. You've essentially trained yourself to automatically respond in that way