My walls are 2 plies of glass weave and epoxy (a scant 1/16 inch), 1.5 thk foam and 5mm (3/16) thk Okoume marine plywood. The trim that came with my windows wasn't going to work with the combined thickness, but by making spacers out of some of the scraps of Okoume (2 extra layers of the plywood with a couple of the individual plies milled off) I will be able to fabricate new flanges out of flat stainless steel sheet metal. By making the spacers out of the same wood as my interior, I can either stain them or paint them the same dark color as other interior accents; and the new flange can be powder coated (or painted) to match the window frame. Far easier to create a flat flange out of sheet stock, than to create a 'Z'-shaped flange. Yes the shim and window flange will sit slightly proud of the surface of the door, but I will "celebrate" the feature with the same finishes, rather than try to hide it.
You could take a similar approach. Cut the thickness of the inside of your window frame down into a pocket around the window opening creating a recess wider than the window frame to allow a flat flange to suit. You might have to experiment some with test scraps to make sure you get the correct finished thickness, after paint, skins, glue, etc., to make sure you get proper squeeze on your window caulk/sealant without having a noticeable gap; or worse, having the flange bottom out without properly squeezing your caulk, but that shouldn't be too difficult. Just make sure that any window cranks or hardware have adequate clearance to operate. Yes, you will have a window ledge, or sill all around your window, but if you treat it the same as the rest of your interior finish it won't look out of place.
In other words, make the thickness of your door where the window goes suit a flat flange, and let the rest of the wall and door be whatever thickness you want.
