Yes, the Tamiya compound will take the black off the top, but it would be hard for you to not polish and/or remove the window trim at the same time.
You should probably do the black trim after the clear, so the trim will stay semi-gloss rather than glossy-gloss.
You can use a toothpick to fill the trim edge lines first, and it will be essentially the same as doing the panel lines for the body. That will give you a definite line to "color" within, and will also give a small margin of error if you slip.