What I would do :
I would remove the corners of the mag holder.
For this, I would make a big cylinder to catch what I want, and use an "intersection" to get only the center. https://piped.video/watch?app=desktop&v=Z3sgFGeoQTs .
Try it first with a cylinder, but actually, I would use a cone or a really big sphere to have a chamfer.
Then I would place my new shape like you on the case. Without the corners, you would not get the troubles of removing the complex shapes for the camera and the buttons.
Do you have some pictures and drawing to explain what you want to achieve?
I agree with the comment about using something simpler than Blender. Blender is the right tool for organic shapes and for sculpting.
What I understand is that you have two models, one for a phone case, one of a "hole" for fixing a magnetic holder.
I use OpenSCAD. With this tool, this would be my logic (could be replicated in other tools :
import the mag holder stl
create a rough shape, like a cylinder, that would fill the hole
make a "difference()" between the cylinder and the mag holder. This way, the cylinder has the shape of the complex hole. You can then use this shape to make a hole in the stl of the case
import the case
import the mag holder once again / or add a volume the shape you want
use "difference()" between the case+mag holder and the complex hole shape to clear the hole
you can enhance this process by creating a negative shape of the buttons holes
The novelty was the story in FPS. Before Half Life, all you have to do is to shoot every moving sprite and grab keys to open doors. The story was a splash screen between the levels.
Nowadays it doesn't look special to have a story. When I first played Half Life, my mind was blown away.
Ouch!
I like OpenSCAD. I was interested in your solution until I found an example. It's way too verbose for me. OpenSCAD has its flaws, but it's simple.
OK that's clear.
What I would do :
I would remove the corners of the mag holder.
For this, I would make a big cylinder to catch what I want, and use an "intersection" to get only the center.
https://piped.video/watch?app=desktop&v=Z3sgFGeoQTs . Try it first with a cylinder, but actually, I would use a cone or a really big sphere to have a chamfer.
Then I would place my new shape like you on the case. Without the corners, you would not get the troubles of removing the complex shapes for the camera and the buttons.