With most default motherboard settings, given the proper cooling and good power delivery, quite a few CPUs (including the 9900k) will still be able to turbo past its base clock.
If your CPU is running at base clock most of the times and occasionally spike to higher frequencies, I would assume that it's because some kind of limit parameter (thermal, power, or otherwise) sometimes decays enough and allows the CPU to turbo up for a moment, but the moment it turbos, it reaches a limit and immediately gets throttled.
As for the harmfulness of the temperature changes... I can only speculate that it shouldn't be much of an issue.
Consider this with laptops: during a normal workload (text editing, web browsing, starting and closing softwares), the CPU temperature varies by quite a bit because those activities do not put a constant and equal load on the CPU.
(This happens opening firefox and loading reddit on a laptop)