In practice, I haven't noticed any loss of throughput due to using Codel on 100ms+ RTTs. Probably most servers now use CUBIC, which contributes to that impression. Using ECN rather than tail drops also makes the delivery smoother.
There is a flaw in your analysis. Codel only starts dropping (or marking) when the sojourn time has remained above target (5ms) for an entire interval (100ms), during which time the cwnd is still growing. Thus the peak queue occupancy is more than 5ms. It is however probably fair to say that a single Reno flow does lose some throughput under AQM. - Jonathan Morton
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