The resulting icon is oversized, even with font-size set to 16px, it looks like 32px or even more.
I used the [Octicons][2] approach to build the icons, so Glyphs setup looks as follows:
My mistake was to create glyphs with setting of "units per em" equal to 1000. After changing the value, already existing glyphs do not update automatically, you should press the button next to the setting.