Was there any follow up to this issue?
I can confirm that ATC does not work using Rpi gateway. Well, it kind of works when you set very low MY_RFM69_ATC_TARGET_RSSI_DBM. I tried -100dBm and then the node is finally decreasing TX power to -2dbm. Anyway, when using Rpi as a gateway I can see (from node perspective) very low (-90) TX RSSI, whereas the same parameter is -26 when using arduino serial gateway (with the same close distance between node and the gateway).
Since the TX RSSI is very low, then the ATC works only when you set your target to lower than that, like mine -100 setting for test purposes.