The latter was done to allow use of larger-than-needed raster (as opposed to SVG) piece images, which then would allow zooming without too much image degradation. E.g. the Diagram in the Minjiku Shogi article uses the 50x50 alfaeriePNG set, but has a 100x100 GIF image for the Fire Dragon.
In the examples you give of where stretching is helpful, the image is larger than the space. So, perhaps you could check the size of each image and apply stretching only if the image is larger than the space.
In the examples you give of where stretching is helpful, the image is larger than the space. So, perhaps you could check the size of each image and apply stretching only if the image is larger than the space.