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"This amounted to 4.5 to 7 million feathers on each bird in Piper"

I'm pretty certain they mean "barbs/barbules for feathers", as in curves (cylindrical tubes fit to curves in 3D space which are normally used to render hair/fur/feathers) making up these feather elements. In other words each feather is made up of hundreds of curve primitives.

4.5M actual feathers themselves on each bird would be absolutely ridiculous and unnecessary.

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You are right -- that's a count of feather curves (quills & barbs), not feathers. We do not model the barbules -- though there has been interesting work done in trying to calibrate a microfacet BRDF for feathers by tracing against barbule-level details.

I would guess they count each frame individually, since the feathers in each one have to be posed and rendered individually.

They wouldn't count each frame individually, as that's not how it's done - they'll have "guide feathers" which are manually keyframe animated, and the feathers in-between are interpolated from the guide feathers (which is how hair/fur is done).

Per frame this just results in different positions/shapes for the curve primitives which make up the feathers.

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