I went over Jetson T5000 and Jetson AGX Orin Series Interface Comparison and Migration document by Nvidia. On table 5 there is a description of the UPHY interfaces migration between Thor and Orion. UPHY0 lanes 4, 5 should be shared between those two Jetsons.
I tried to validate it in two different ways:
Compared the SoC net name on the two chips
Compared the functionality of those nets on the EVB schematics
I found the following gaps:
UPHY_RX4_N/P (Thor) should be connected to HS_UPHY0_L4_RX_N/P (Orion) but actually connected to HS_UPHY2_L0_RX_N/P
UPHY_RX5_N/P (Thor) should be connected to HS_UPHY0_L5_RX_N/P (Orion) but actually connected to HS_UPHY2_L_RX_N/P
Table 5 is correct in Jetson T5000 and Jetson AGX Orin Series Interface Comparison and Migration guide and so are the carrier board schematics for AGX Orin and Jetson Thor carrier boards.
Migration guide provides path to attain compatibility between both designs, the pins used might be different however you can still get functional equivalence using different set of pins on both the Jetson modules and some adaptations would be needed in the carrier board design to achieve this.
So if I understand correctly (and i will appreciate your confirmation): Table 5 discuss about interface migration but do not promises pin compatibility between them