We are facing a similar issue but out use case is nested entity.
we have the below nested entitties
child1Entity is child of ParentEntity and parent of child2Entity. Child2Entity is child of child1Entity.
when we add deltaImportQuery on child2Entity. It is not executing deltaImportQuery during delta import.
I found that below code(#503) in the DocBuilder class is restricting the deltaImportQuery from not being executed at the nested child entity level.
for (EntityProcessorWrapper child : epw.getChildren())
child.getEntity().isDocRoot() ? pk : null, child, false, ctx, entitiesToDestroy);