Because designers, that's why.
Beta sites are given a temporary icon, consisting of characters or small icon representing the site name or topic, on a blue speech balloon modelled on the Stack Exchange logo. Pictograms are used where one is available (like for Chess SE, the rook is an obvious choice), a one- or two-letter abbreviation otherwise. The Craft CMS SE site got the same shape in red with a
C in the same font as the typical branding for that CMS instead of a pictogram, presumably because a plain
C on blue could have meant anything.
When a site graduates from public beta to full release, it is given a full-on unique design, which includes a site logo. A Stack Exchange designer first proposes a design on the site's Meta, and the final design is then created based on the community feedback. See the Mathematics design proposal for example, where Jin briefly explains how he picked the logo.