Yes it is, it is the PCIe switch that feeds the two miniPCIe slots. The U-Boot boot sequence only displays the link status for devices directly attached to the CPU.
My guess is that there is an issue with the second PCIe lane on your JMB545 card and that is why it won’t link up in the M.2 Key M slot.
The smaller SATA controller card is only a single lane, and the M.2 Key B slot is also only a single lane.
Do you have any other M.2 Key M devices that you could use to check if the Key M slot is working correctly? An NVMe SSD would be the best one to test as they always have two or more lanes.