I asked a similar question before when JP5 was still only early access.
I am trying to use PCIe C0, on UPHY lane 0 which is normally set to USB 3.2. I can change the UPHY mode in the pinmux just fine but the sideband signals are not available. Refclk and PERST/CLKREQ cannot be set in the pinmux, even though it is listed as supported in the design guide.
Will this be added at a later date? I would like all of my mPCIe slots to work.