So that's the entire south side of the PHY verified correct levels.
Now let's check the west side where MDIO addressing is configured.
RX_D2/SGMII_RX_P = 561 mV = 0.31x Vdd. That's wrong, it's between the mode 3 and mode 4 strap ranges.
I have no strap resistors on this pin and it's AC coupled to the FPGA (so any biasing coming from the FPGA shouldn't affect it, I'm probing at the PHY side of the coupling cap).
Per datasheet it's supposed to have a 9 kΩ pulldown in strap mode, and be max 0.098x VDDIO if left floating (strap config for mode 1, which is what I want).