If you are putting what is essentially a plastic "plug" in an opening in an aluminum body, as T.Albers says it should be the same thickness as the body shell to ensure it's flush with the exterior surface. With this sort of exercise I have found that it's best to put a backing on the "plug" that extends past its sides to ensure it's held in place - otherwise you are relying on the small amount of glue that gets between the plastic and the shell to hold it in place. If the shell and the new piece are flush on the outside, the amount of filler that should be necessary to cover any gap between the shell and the plastic on the exterior side of the car should be limited and not cover the plastic surface.
All this also relates to a subject we have not discussed, which is how these mods look when viewed through the windows on the other side of the car. (I always find that visitors will peer inside of any lighted passenger with a full interior and at such close range all manner of things become visible.) You can't do much to conceal them other than to paint them the same color as the inside of the shell was to being with, which with aluminum shells from Lionel and K-Line was usually standard interior cream or light green. Many prototype streamliners had wood panelling on the interior walls but I have not tried to duplicate that (yet).
Some window inserts can't be concealed and basically you have to live with them. All of Lionel's 21" ABS cars fall into this category. Earlier models with window strips are a lot more forgiving.
