I’m still not clear on the topology here.
Do we have two endpoints here? Or only one endpoint? As I mentioned earlier, on Jetson-Xavier, one slot is owned by one controller and each slot has its own PERST#, CLKREQ#, REFCLK, and Tx/Rx lanes. If you are using PERST# from another controller, then, by the time the endpoint device observes a low->high transition on PERST#, it may not have REFCLK available. That could be one reason for the link not coming up.