I'm not saying they should hold upgrades until the gate, just showing the complexity in calculating any one person's profitability. Your examples are a great example of why this can be such a tricky exercise.

But if I were trying to calculate the opportunity cost, it certainly wouldn't be the difference between full J and full Y. It would be more like the difference between the average price for J on the route and what the person actually paid for Y.

I suspect that pushing all upgrades to the gate would have a very negative impact on the sale of fare classes higher than Standard, as well as FP sales, so I don't think that's likely.