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I'm not really sure of this. I think the latency is there anyway, even sending/receiving bigger blocks. But of course with bigger blocks it becomes less importand.
I think it has to do with the oprating system behaviour, more than with the USB-protocol itself.
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The latency timer, the one that you can change with the API, is a timeout value. The idea is to not send a packet immediately after receiving the very first byte, because otherwise it would send single byte packets, very inefficient. It specifies the timeout that once expired, the device will send a packet even when the buffer is not full. Then it doesn't affect packets that fill the 64-bytes buffer.
It has no relation with the operating system behaviour at all. This timeout controls only the transmission from the remote end, where the actual chip is located, to the PC. It doesn't affect transmission from the PC.
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