If you use a spring loaded diamond drag tool, the spring compression may be enough to cover the change in elevation I have one with 3/8" compression. My experience with acrylic has been that the amount of compression makes very little difference in the lines. I don't know how well the aluminum cover will engrave with a diamond drag tool, however.
Best would be if you can find a scrap side cover to experiment with. Let us know what you end up with.
Good judgement comes from experience.
Experience comes from bad judgement.