Zymkey would be able to provide a stable time reference when your host computer boots up. From that point on, you can reference the time using the standard libraries (e.g. time function call in C or date command line utility). However, the host pi clock will continue to drift independently after the boot-time reference is obtained from Zymkey. Another option would be to call the Zymkey API to get the clock in C/C++/Python.
We don’t expose an API which would allow one to set the Zymkey RTC since Zymkey is considered to be a secure device. Instead, an interface daemon determines when NTP is synchronized and enabled and sets the time from the current system time.
Hope this helps.