My suggestion is to add a Color Key effect, and using the eye dropper tool choose the color of the remaining edge. Then play around with the settings to adjust tolerance, thickness, and feather amount.
If duplicating your comps solves the issue, you could look at a free plugin called true-comp-duplicator on aescripts which allows you to duplicate the comps easily without replacing the nested comps individually. Here is a link: https://aescripts.com/true-comp-duplicator/
To control what you see on stage using a drop menu, you can use a Drop Menu Control effect and connect it using some expressions. There is a very good tutorial on this topic that could be useful to you: https://youtu.be/nPTNtwSx9SE
I hope this helps.
Jerard.
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