The verb ‘to lie’ has two past tenses, for different meanings of the word.
He lies all the time. (Says something false, present/timeless). He lied yesterday. (Said something untrue in the past)
He lies on the bed once a day. (Puts himself on the bed, present/timeless). He lay on the bed yesterday. (He put himself on the bed in the past.)
The book is a classic written for small children and is written with the simplest English tense, the past.
As far as whether it’s natural, natives often confuse lay/lie and to my ear the past tense of lie, second meaning, sounds a little awkward, and would surely sound even more awkward if I hadn’t heard and read this very book thousands of times.
Colloquially we very well might say ‘was lying’ to avoid that awkwardness. But using that here would destroy the beauty of the work!