How does one go about marking food in an oven?
I have spent decades cooking for people who can't have gluten, and I and several other people can't have shrimp. The simplest thing to do is to make everyone's food meet the needs of the allergic person. So for example don't bread anyone's chicken, or make a single gluten-free gravy. 

That's the simplest, but it may not meet your other needs. In that case, I avoid anything that can fall off or be missed. In the case of chicken pieces on a baking sheet, I would use one large sheet and one smaller pan, and put the special portion on the smaller pan. Now you can flip and turn the pieces freely, and you don't need to worry about the juices mingling or whatever. I do this when cooking regular and gluten-free pasta, for example; I use very different-sized pots. When I run a separate butter dish to avoid crumb contamination, it's not two identical white butter plates, one of which is labelled; it's a white plate for the might-have-gluten-crumbs butter and a small clear bowl for the keep-it-crumb-free butter. These visual cues are much larger than a toothpick and can't be missed or fall out or end up on the underside or whatever.