Earlier quoted context omitted.
This semantic variability in the relation between the two nouns of a compound is pretty common in compound nouns: "Y made of X", like "tomato paste", "Y used (somehow) for X" (like "toothpaste", "paintbrush", "electrical outlet"--here an adjective, but still a lexicalized phrase), "Y in X" ("treehouse"), "Y for X" ("doghouse"), "Y containing X" ("paint can"), not to mention metaphorical uses, with some etymological r…
“Windows Subsystem for Linux” is probably the most confusing example of this (an environment subsystem which provides a Linux userspace to a Windows NT kernel). more intuitive would be to call it a Linux Subsystem for Windows, but presumably for branding purposes they wanted Windows in front.
Linux Subsystem would be completely wrong, because it is a Subsystem of Windows not of Linux.