I saw a block diagram of a Mindspeed 4 channel CDR, that has Data inputs and Clock + Data outputs. Clock means recovered clock in my understanding.
As I previously mentioned, the PCIe Refclk can be used as a trigger for jitter measurements, because all Tx signals are phase locked to it. See also PCie 2.0 Base Spec chapter 4.3.2.
jitter budgeting and measurement for a discussion of the PCIe jitter model.
If you use REFCLK as a trigger, you see the transmitter fully contributing to measured jitter. But I don't think that this is a problem in comparative measurements.