The link is gone and I haven't seen these cookies. But I assume the cookies are the same material throughout, except that some is colored differently in order to make a face. I always assumed stuff like this is made by extrusion when the dough is warm and pliable. In the extruder, there are die injectors placed at the correct spots releasing just the right amount of die to bleed into the correctly sized 'blob' to make the facial features. For a smile, they need a row of die injectors but the individual injectors would have to be in a staggered row so as to allow the dough to reform around the leading injectors before remaining injectors can die their part of the 'smile'.
iv not seen the biscuits eithor.. but, ya cant just inject dye like that, it would be very inconsistant in shape and colour, if they have clean edges, odds are its eithor made manually at large scale, then reduced in size via extrusion... or (and this would be my guess) the dyed mix is injected into the center of the flow of undyed mix under presure (its streaming past, so you can just stick an injector into the flow and pump in the coloured goop, then just let the presure take care of the rest)
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