I'm not sure if I missed a setting, but it appears that ufo2ft.compileVariableTTF doesn't implement the OVERLAP_SIMPLE / OVERLAP_COMPOUND flag that FreeType relies on to render overlapping paths correctly.

More information on the issue here: microsoft/cascadia-code#350

For Cascadia Code, I adapted this code in my build script to resolve this issue:

def overlapFlag(varFont):
    
    glyf = varFont["glyf"]

    for glyph_name in glyf.keys():
        glyph = glyf[glyph_name]
        # Set OVERLAP_COMPOUND bit for compound glyphs
        if glyph.isComposite():
            glyph.components[0].flags |= 0x400
        # Set OVERLAP_SIMPLE bit for simple glyphs
        elif glyph.numberOfContours > 0:
            glyph.flags[0] |= 0x40
    return varFont

Is this functionality available in ufo2ft? Else, where would be the best place to implement something like this?