> The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

The license is saying you have to retain the license itself; it doesn't say anything about any other attribution notices that exists in the source files or anywhere else. It doesn't specify where you have to put the license; it could be in a comment in the code, or it could be in a file next to the code, and that doesn't change anything about the terms of the license.

If the original author put the license in comments, you can keep it in comments, but you could also move it to a standalone file. If the original author put it in a standalone file, you can keep it there or you can move it to a comment, but you can't remove it. If you distribute a compiled binary, you need to be sure you're including the license alongside the binary as well.

If Microsoft distributes a "substantial portion" of the software, and they do not include a copy of the original license (including the copyright statement at the top attributing the original author), they're in violation.