Do you know if the originally supplied Fritzbox received a firmware update coincidental with the reduced downstream throughput.
I ask because by default these updates are enabled by and supplied from the manufacturer, though I think you can change the settings for busy times or notify-only or not at all.
It's possible that a later firmware combined with migrated config could result in some built-in QoS being active, which could favour low latency over sustained download throughput for example.
With asymmetric connections and a sequential test, during the upload test there is often plenty bandwidth for the ACKs (returning downstream) such that QoS does not need to kick in.
Otherwise I'd wonder if it was something else affecting PPPoE hardware acceleration (as a computer doing the PPPoE itself generally has more than enough CPU to handle it purely in software while a low power appliance relies on some kind assistance - may be called fast path or offload processing for example.
prlzx on Zen: FTTC (VDSL) at ~40Mbps / 10Mbps
with IP4/6 (no v6? - not true Internet)