Hi! This seems to be a bug: if you add a component, which has special layers, but don’t duplicate those layers to the glyph, the width of special layers is ignored in a variable font:
Left: original O with a special layer;
RIght: component ‘O’ without special layer duplicated
Yes, this is a known bug (at least in older versions of Glyphs). I think somewhere around 3125 this was fixed, at least theoretically.
Annoyingly, in later versions, if you keep the fix used for older versions, it breaks, and if you remove the extra special layers in composites, the anchors (and metrics) don’t work anymore.
I had to resort to decomposing composites with special layers, or using an older Glyphs version.