Hi,
Based on my experience, it is recommended to use CLKUSR for transceiver calibration only. In user guide, there are some cases where you need to perform recalibration in user mode as well.
However, I am currently consulting Factory if it is possible to use the CLKUSR pin for XCVR and core logic at the same time without any potential issue. Also, I am seeking clarification on your Q2 from them as well.
I will keep you posted on the progress by end of the week or as soon as there is any valid response. Please ping me if you do not hear back from me.
Thank you.