Workarounds for "cp -p" not preserving nanoseconds on High Sierra with APFS?
Good to know that I'm not the only one who thinks this is a problem. I ran into it while writing a Python script for monitoring parts of my macOS (10.15.7) filesystem, which also involved coping files. The script sometimes behaved erratic and produced unpredictable output. After some poking around I found out that the incapability of cp -p to preserve nanoseconds is the core of the problem.
One workaround for your problem (but not for mine) could be coreutils: gcp -p behaves as intended.