Well, it's not like Microsoft deliberately disabled the support of Noto Emoji. More simply it just outright does not support the format that Noto uses.
While almost all fonts you deal with are OpenType-based, there are several different colour-font extensions to OpenType – Segoe UI Emoji uses Microsoft's own format (layered vector drawings in COLR/CPAL), while Noto Emoji Color uses Google's own (bitmap images in CBDT/CBLC). There's also Adobe's "SVG " and Apple's "sbix" format.
Noto is originally drawn in SVG format, so it includes Adobe's "SVG " table alongside Google's bitmaps, because that's simple enough. But the Microsoft layered format is quite different, so I'm not sure if automatic conversion would be easy or even possible.
See also issue #43 "NotoColorEmoji.ttf not a valid font in Windows" on GitHub for a more detailed explanation.
A while ago, there used to be an "Adobe Type Manager" adding support for Type-1 fonts, back when Windows only supported TrueType. But I haven't heard of anything that would add support for different kinds of emoji fonts...
Maybe you'll like the new Segoe Emoji that Build 14316 brings?
Update: Microsoft says that the 2016 "Anniversary" update finally supports all the above formats.