The transparent rectangles in the downloadable SVGs are for sizing. When people used apps like Sketch to create mockups, the SVGs weren't sizing properly because Sketch had no way to understand that there needed to be some space around the icon.
Additionally, icon fonts rely on the PUA to render their glyphs. Given the emoji explosion over the past several years, that PUA is getting harder and harder to assign glyphs to.
I can't be the only one that's visited a site on my phone and found emojis where an icon font glyph was meant to be.