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The throughput is the same: 3 jobs in 9 days.

You mistake the thoughput for the latency. The latency is smaller (less time from start to end) in the AAABBBCCC approach.

The reason ABCABCABC can be slower in a computer is that context switches takes time, and AAABBBCC has only 2 context switches whereas ABCABCABC has 8.

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Slower in a computer, slower yet in people.

And the throughput in AAABBBCCC is 1 project in 3 days, where ABCABCACB has a throughput of 0 projects in 3 days. In a business where cashflow is important, that 3 day throughput is more important than the overall 9-day throughput.

That's a good point, if you're taking into account cash flow and exponential return on cash flow, then having projects finish sooner and start generating cash flow and interest sooner is preferred. Fewer context switches also contributes to that.

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