Redundant superclass in ontology after reasoning (owlready)

Question

I try to understand the rector-normalization-technique for ontologies in detail. I use owlready to implement the examples.

The article recommends to have a asserted single inheritance structure and introduce multiple inheritance by inference. As example it uses classes as Protein, Insulin, and Protein_Hormone, Hormone_Role.

Asserted facts:

• Insulin is_subclass_of Protein
• Insulin plays_role Hormone_Role
• Protein_Hormone is equivalent to (Protein and plays_role owl:someValuesFrom Hormone_Role) (defined class)

After the reasoner ran, Insulin is correctly recognized as subclass of Protein_Hormone (expected result).

However, it is still classified as direct subclass of protein. This relation I deem redundant because every instance of Protein_Hormone must be a Protein by definition. Also, if I apply Protegé, the inferred class structure does not contain this redundant relation, as shown here:

Is there a (canonical) way to get rid of this superfluous subclass relation?

Alternatively, why is my suspicion of superfluousness wrong?

Code for this problem (see also this notebook for outputs):

import owlready2 as owl2

# rme: rector-modularization-example
onto = owl2.get_ontology("https://w3id.org/yet/undefined/rme#")

with onto:

    class Protein(owl2.Thing):
        pass

    class Insulin(Protein):
        pass

    class Hormone_Role(owl2.Thing):
        pass

    class plays_role(owl2.ObjectProperty):
        pass


    class Protein_Hormone(owl2.Thing):
        equivalent_to = [Protein & plays_role.some(Hormone_Role)]

Insulin.is_a.append(plays_role.some(Hormone_Role))

# before reasoning
print(list(Protein.subclasses()))

owl2.sync_reasoner_hermit(infer_property_values=True, debug=1)

# after reasoning
print(list(Protein.subclasses()))