I haven't noticed that, but I'd propose an alternate explanation: the amount of time it takes for you to notice a CPU spike, get annoyed by it, and launch task manager ends up being just slightly shorter than the running time of some common CPU spiking tasks.

oh yeah, I caught addressbooksync maxing out four cores for about a minute on htop before.

I just keep activity monitor open all the time. I've noticed that fan speed significantly lags CPU load, so it's difficult to notice and react in time. The one that gives me the most trouble is mds_store, or the spotlight search indexing process. I disable indexing on basically the whole drive but it still spins up the fans every once in a while.

If Activity Monitor runs with a higher priority/niceness, that could explain it

On Windows some scheduled tasks are scheduled to run whenever the system is idle, and seem to stop running when the system is being used again (e.g. by opening a task manager). Maybe the same is true on Mac.

This behavior does make one think of malware. It's frustrating when the core features of an OS thwart user monitoring and control, even if inadvertently.

100% this on my rMBP 2015. Almost every time too. I notice my PC will give a similar 'system interrupts' reaction with Task Manager, however.

Yep, many many times on my 2017 MBP. Far too consistently repeatable to be coincidence, IMO.