alt Hacker NewsThis, and it may have also been a legal thing. "Product for Third-Party OS" has been accepted as a descriptive use of a third-party trademark for decades, requiring only proper attribution rather than a license, whereas marketing a product that didn't even originally use the Linux kernel as a "Linux Subsystem" might have been considered riskier by Microsoft's lawyers in spite of the nonstandard use of the former.
It could be even more simple. Microsoft would want to their own product, Windows, to come before Linux in the name.
I read through the brand guidelines where I work, and we have a similar stipulation. Maybe there is some law mixed in there, but from a pure branding play, a company will never want to put someone else first.