The core of the software is a subsystem, specifically a Windows subsystem; you're not running this subsystem on macOS or FreeBSD.

The "for Linux" is added because it's a subsystem for Linux applications (originally not leveraging a VM).

Microsoft also had the "Microsoft POSIX subsystem" (1993) and "Windows Services for UNIX" (1999) which were built on the "Subsystem for Unix-based Applications" (rather than "Unix-based Application Subsystem"). That chain of subsystems died at the end of Windows 8, though.

There are many reasons not to put "Linux" in front, but the naming is consistent with Microsoft's naming inconsistencies. It's not the first time they used "subsystem for" and it's not the first time they used "Windows x for y" either.

The naming is ambiguous, you could interpret the Windows subsystem for Linux as a subsystem of Linux (if it had such a thing) that runs Windows, or as a Windows subsystem for use with Linux. Swapping the order doesn't change that.

In other languages, the difference would be clearer.