In order to understand this, you need to study the process of Samantabhadra's liberation. When you do so, you will discover than Samantabhadra was not always liberated. Then you will understand that Samantabhadra possessed innate ignorance, but not imputing ignorance. Innate ignorance is simply unknowing. Imputing ignorance causes dualistic vision.
Where can I read about the process of Samantabhadra's liberation? I could not find antything like that in the Kunjed Gyalpo, can you point me to the passage saying about this process?
In conclusion, at the end of this book ChNNR says Samantabhadra was never stained, nor it would know the limiting concept of liberation, or "first".
The process of the liberation of Samantabhadra is proper to man ngag sde. You will not find anything about it in sems sde, at all, not even a little bit. You can read about it in the eleven topics of Dzogchen Nyinthig.
The innate ignorance is not a "stain" per say. It is not an afflictive ignorance, it is a simple absence of knowing.
Basically, at the point the basis arises from the basis, there is a neutral awareness present in the basis. That neutral awareness has no self-knowledge until the basis arises. While it is not aware of itself, it is in a state of non-afflictive ignorance.
When it apprehends the five lights, it apprehends them either as its own display, resulting in nirvana, Samantabhadra, etc., or it does not, resulting in samsara. The Tantra That Uproots Delusion:
Knowing the energy of the svābhavakāya
as their own appearance produced buddhas;
being mistaken about their own appearance produced sentient beings.
Afflictive ignorance comes from the dualistic vision produced by imputing ignorance.