Use of the English language can often lead to ambiguity.

In the case of "Windows subsystem for Linux", it can be reasonably read that "for Linux" means that the functionality applies to Linux, i.e., to provide it with a subsystem that gives it Windows functionality.

Similarly, in the case of "Linux subsystem for Windows", it can be reasonably read that "for Windows" means that the functionality applies to Windows, i.e., to provide it with a subsystem that gives it Linux functionality.