In (non-animated) PNGs the image data is contained in IDAT chunks. In APNGs there are IDAT chunks, which contain the default image, and fDAT chunks, which contain frames of the animation. The default image is sometimes part of the animation (as the first frame), and sometimes not (displayed only by non-APNG aware viewers).
The default image must have the same size as in the PNG header chunk. But the fDAT images can be any (smaller) size. So the first frame of a PNG is allowed to be smaller than the whole image size so long as we are in an APNG and the first frame is from an fDAT chunk, not an IDAT chunk.
We post transparency if we encounter this case because we don't draw into those pixels on at least the first frame.
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