Because the "center" of the G is not the optical center. Same reasons as everything else in the original article. Take a look at the image at the top of this page: https://en.wikipedia.org/wiki/Typeface_anatomy. The crossbar of the E (and R) are higher than vertical middle. And they differ from the x-height.
Despite your affinity for geometry, geometric fonts are the exception, not the rule. And even geometric fonts often have tweaks that make them less "perfect" geometrically but look more correct. https://en.wikipedia.org/wiki/Sans-serif#Geometric
I found some hints - straight from the source, Google's design team - to the reasoning behind the "G" design, and why the alignment of colored arcs turned out that way.
Thank you for the pointers. I see, "perfect" geometry is not necessarily good typography, and that these "imperfections" have reasoning behind them, for legibility, better balance, to give more natural/correct feel.
I can understand the "near-perfect" circle, but wouldn't you agree that the (mis)alignment of the green and red arcs' edges feels wrong? Not about typography/legibility, but about the balance of lines. Interestingly, in the Futura font, which is quite similar to Google's Product Sans, the top line of the G extends a little further, so that its edge would have lined up "perfectly" as I would have preferred. For comparison: https://qph.ec.quoracdn.net/main-qimg-4c522c183600dbc2ede9aa...
Despite your affinity for geometry, geometric fonts are the exception, not the rule. And even geometric fonts often have tweaks that make them less "perfect" geometrically but look more correct. https://en.wikipedia.org/wiki/Sans-serif#Geometric