[ahepp]

I think we are talking about things like interrupt latency, not NTP synchronization.

MCU interrupt latency can be extremely deterministic. I ran some measurements for work and found Linux to be adequate for many uses, but it is a valid concern. There are some Linux kernel patches like PREEMPT_RT that attempt to bound Linux latencies, but generally MCUs are a lot better suited if latency is critical. In part because they just have less software running on them to interfere with timing.