The pilot is not flying the plane at cruise, the autopilot is.

The autopilot can definitely have an effect on how smooth the flying feels, depending on how autothrottle and altitude hold control loops are implemented.

My understanding is that pilots frequently fly parts of the cruise so that they have adequate "stick time" to stay fresh and familiar with the machine.

Probably not the actual cruise (30k+ feet at M0.7+), but definitely some of the nicer approaches and departures. Hand flying an airliner in cruise within the tiny strip of air it’s allowed to fly in (google Reduced vertical separation minima) is no fun.

Pilots are still doing a job, and sometimes that job involves keeping their skills fresh and honed, or working around a partially non-functional or degraded autopilot. Sometimes it's even a matter of personal preference, with some pilots preferring more hands on time than others.

I’m not sure if you’re disagreeing with me, so I’ll expand on the previous post: most commercial flights cruise at altitudes where it’s not allowed to fly without autopilot. Not for honing the pilots’ skills, not because of a malfunction.

There are parts of the flight where hand flying is allowed, but those are the parts closer to the ground (or on very short hops where the cruise altitude is significantly lower than usual).

Flying an airliner by hand at cruise is dangerous and usually constitutes an emergency. ATC expects the plane to stay precisely at its assigned altitude, especially in RVSM airspace. It's difficult to keep that altitude by hand at speed. Cruise is also normally done close to the edge of the plane's abilities, so small deviations can have catastrophic effects (overspeed or stall).

Pilots routinely do climbs and descents at lower altitudes by hand to practice their skills, but not cruise. See this Airbus doc: https://safetyfirst.airbus.com/high-altitude-manual-flying/