Having your hardware run Windows and having your software interoperate with Windows are wholly unrelated technical issues. The hardware and software are designed by different teams, and the hardware people aren't likely to be of any help to the software team.

The original complaint seems to be about interoperability of Windows PCs with non-MS server software. In 1998 Microsoft had yet to release a formal specification for the CIFS protocol, which was a revamped version of the SMB protocol (basically: what Windows uses to share files over a network). Andrew Tridgell created a port of SMB services called Samba in the 1990s which allows non-MS systems to act as clients or servers when working with Windows clients or servers. MS created CIFS as a response but both held back on specifications (after initially submitting them to the IETF for standardization, then withdrew them) and allegedly onerous licensing restrictions which appeared to prohibit use or porting of CIFS to open/free software.

The net result has been that SMB continues to be used for interoperable file sharing between Windows and non-Windows environments. CIFS has been sort of reverse-engineered by Samba developers but it's not clear that it's actively used. With respect to the EU case, it may be moot: most organizations have standardized on SMB for interoperability, to Microsoft's chagrin and detriment.

It is sort of like if Tim Berners-Lee had --upon realizing the rapid uptake of his web protocols (HTTP, HTML)-- decided to withdraw, create even better (more secure, robust, whatever) versions of those protocols, but with onerous licensing terms. Without a doubt the new versions would be "better", but due to the licensing restrictions no one implements them.