I still find it curious how few holes there are (took a while to find one!), and finally figured out why: imagine a large square grid. It would probably have a different density than the rhombus grid, and it seems nontrivial to match it up. It seems that in the code this is done by each rhombus having edge length 50 while the periodic table elements are 38 x 42 pixels in size.
This, if I understand it correctly, means that this tiling is not just aperiodic but (in this regard) also anisotropic -- it's denser in one direction than another. And thus I have learned a new thing about Penrose tilings. :)