Stencil Example

Here we are in Modeler, showing the geometry of the cylinder and the boxes we're using for this example.  Notice how the box on the left in the lower right hand view doesn't have any geometry lines close to it on it's left or right.  Also notice how I've used the knife tool and sliced more geometry close aboard to left and right of the right hand box.

Here's the open gl view inside Layout of two versions of the same cylinder.  The basic geometry of the cylinder is unchanged, except for where I did the stencil of the box, followed by a smooth shift to recess it like a doorway or airlock.  Right away you can see on the lower one how we're going to have artifacts due to the left and right sides being unsupported by close-by geometry.  The upper one doesn't show any such problem.

And here's what a simple, un-textured render looks like.  Big nasty artifacts on the lower one, none on the upper.  The same theory will work for spheres or other complex - compound shapes, it's just harder to make it work.  With those types of shapes you usually will have to sub-divide and or triple the polys that will be affected by the boolean or stencil/shift.