How to non-destructively bevel and extrude a mesh intersection? In Blender 2.93/2.92, I am looking for ways to more easily create hard surface structures with doorways/archways that are extruded above the surface, in a non-destructive way that allows for quick prototyping.
When trying to use the bevel modifier on a boolean object, the bevel profile only cuts in to the surface.  Is there a way to use modifiers to get the beveled edges to extrude above the base surface, using the boolean modifier?
Reference screenshots.

A cube with some extra lines cut into a face. Faces inset where hole is desired.
Extruded the boundary face-loop above the original surface. Extruded the inset faces below the original surface
Unsuccessful attempt at creating this non-destructively. Bevel after boolean difference only cuts &quot;in&quot; to the surface, does not create any geometry &quot;above&quot; the surface
If I understand your problem correctly, you should be able to solve this by using the bevel modifier limited to a vertex group.
First, go to the Object Data tab in the properties pane (the green one, can't miss it) and open Vertex Groups.  Hit the &quot;+&quot; button to create one.

Then, select the vertices you want to bevel in Edit mode.  While the group you just created is selected, click the &quot;Assign&quot; button underneath the vertex group list.

Third, go to the Modifiers tab (the one with the wrench) and add a Bevel modifier.  In the &quot;Limit Method&quot; drop-down, select Vertex Group.

Finally, select the vertex group you created earlier.  Play with the numbers a bit, and you should be good!