You could try to play around with various kind of buffers. It could be that throughput is limited by buffer sizes on upload or download side. It should only make a big difference on very fast lines though.
Bigger buffer cause more data to be transferred at once, but raise memory and system load.
Additionally Phex is not really optimized for a single high speed end to end transfer like SCP is. There is a quite big overhead to mange segments, sync transfers and handle multiple connections.

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