I ended up with a 103-key Unicomp New Model M (essentially the same layout as a 101-key, but with one Windows key and one context menu key stuffed into what would have been the small blank spaces in the bottom row between ctrl and alt—I really wanted a full-length spacebar). Linux is most often installed onto ex-Windows PCs, so it’s hardly surprising that it expects the Windows keyboard layout.
(I believe the current generation of Gnome devs is big on minimalism, AKA omitting or removing features. I can understand the appeal from a code maintenance point of view, but it’s never been a DE that I liked.)
You can buy keyboards with replaceable keycaps. You can also buy keycaps with Tux logos on them for at least some of those keyboards. You can decide for yourself whether your aesthetic dislike of the Windows logo is worth the rather higher price of such a keyboard.