In general, NTP is a time sensitive process, and application processor/SoC are indeed going to have far greater rates of clock slips than an MCU running off an XTAL or TCXO.

RTLinux has a module feature to sync the scheduler to an external pin state. It is an obscure feature...

Adding more processors creates a well-known named-problem with metastability:

https://en.wikipedia.org/wiki/Clock_domain_crossing

Real-time is not guaranteed latency, and the Pi is not like Zynq fpga. =3