During the 2.93 to 3.0 transition, instance handling was made more
explicit in general. However, we forgot to change the boolean node,
which still implicitly gathered all the instanced meshes and fed them
to the boolean algorithm separately. We waited for the next breaking
release, 4.0 to "correct" this, and did it in fc06a471f1.
However, in that commit it was assumed that the "Self Intersection"
mode would be able to address the use case. The idea was also to push
some complexity outside of the boolean code, which is already one of
the more complex areas in Blender. Though it's possible to have a
"Group ID" or "Shape ID" input in the future as well, it's also
reasonable to expect some instances to be processed by the node,
even though it isn't quite consistent.
This commit makes a compromise by processing meshes contained by
top-level instances. We do it at this stage of the release to avoid the
breaking change.
Pull Request: blender/blender#114632