The whole "philosophy" is that the base represents the "mass", the inner squares (on the very rim + completely inside) represent cuts, while the outer ones represent extensions (found within "alternates"). If we were to enlarge the squares significantly, we would see clear letter shapes. On the other hand, numerals for regulars have outer squares, and for "alternates" they have inner ones in order to make a clear visual difference in the typeface. Alternates are "alternates"because they imply an additional rule, due to the mentioned extensions. The goal is for all inner squares to be positioned on the rim, but for ease ofreading there are variations where they are completely inside. When monochrome,there should always be space between glyphs.
The default color of the "color" version is with red squares. If you want to change the color, just play with the hue/color range options.
