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Yes, all done by hand. I usually started with 64 colours, then added more as I needed them. The big difference to low colour pixelling is that instead of re-using existing colours I'd create a new one just to give a bit more colour variation.
That's just something we Amiga pixellers did in our day, and spending 50-80 hours on a fullscreen pic was normal.
In fact, I don't even know about index techniques. I did use auto-antialiasing in some of my later pics for hair and alike, but it was always too messy to use regularly - at least on the Amiga.