Well, sometimes there are design reasons to use something that seems counter-intuitive. I can't say why Microsoft would choose to do this but there are possibly several reasons. You can't always go by what the science says because if we did then all designs would be roughly the same; whatever science says each element should look like. If we followed the suggestions from your linked article then all of our elements, especially buttons, would be circles.
Sometimes, for the sake of the design, you would choose harsh corners so that it makes them stand out all the more. Especially since so many use rounded corners for their designs these days. When everyone else has rounded corners your squared corners stand out. They may be bothersome to the eye but they attract the attention.
Maybe having rounded cornered buttons conflicts with the rest of the design which ruins the pleasing effect of the entire design? Possibly they felt breaking the "rules" for the buttons prevents a collapse of the design as a whole. Say, for instance, the majority of the design is squared corners but those rounded cornered buttons stand out so much that the eye is constantly draw to them instead of the content to be read?
Maybe they just don't like rounded buttons?
As someone else commented, maybe they don't want their buttons to be too similar to buttons from another design? It does seem you can be sued for minor design choices these days.
Sometimes, for the sake of the design, you would choose harsh corners so that it makes them stand out all the more. Especially since so many use rounded corners for their designs these days. When everyone else has rounded corners your squared corners stand out. They may be bothersome to the eye but they attract the attention.
Maybe having rounded cornered buttons conflicts with the rest of the design which ruins the pleasing effect of the entire design? Possibly they felt breaking the "rules" for the buttons prevents a collapse of the design as a whole. Say, for instance, the majority of the design is squared corners but those rounded cornered buttons stand out so much that the eye is constantly draw to them instead of the content to be read?
Maybe they just don't like rounded buttons?
As someone else commented, maybe they don't want their buttons to be too similar to buttons from another design? It does seem you can be sued for minor design choices these days.