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You can pull the frequency of a crystal resonator circuit by changing the loading capacitance, for example. You may use a varactor or any semiconductor junction. Doing so doesn't really affect phase noise.

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I'm probably missing the right terminology. I would have thought the feedback loop creates jitter of its own. Phase locked VCOs are generally noisier than a crystal alone. But maybe I'm overthinking it and the loop bandwidth can be made very narrow with trimmed crystal and long integration times or whatever.

Your own answer is right. For atomic clocks, the integration times of the feedback loop are typically much longer than a second.

The contribution of the crystal to the overall tank circuit Q is vastly higher, by several orders of magnitude, than the contribution of the varactor diode.

So while making an oscillator steerable inevitably increases its phase noise slightly, the increase is either ignorable in practice or cancelled by the control loop itself.

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