Referring to the NIST classification of semantic relations, general affiliation is a different relation than part-of. That's why conflating them is not the best idea.

But this is a minor issue in that context. I am wondering if there is any list of "properties for beginners", that should not be treated as a real part of the knowledge base?
As I wrote earlier there are two problems with ambiguous entities:
1. indicating super-properties
2. inferences drawn with such properties

I don't question the usefulness of properties such as "country", i.e. searching all cities in one country or searching all bands that originated in another country.
I am just concerned with the duplication and as a result coherence of the data that is in Wikidata. One of the basic principles of DB design is that data should be stored in only one place. That's why DB normal forms where developed. Even more - that's why Wikidata was extracted from individual Wikipedias in the first place!

In the case of Dublin, country and Ireland. At present we have two distinct claims expressing the same fact, that one day may become incompatible.

Being constructive - maybe it's the time to consider derived properties? Thus claims like "Dublin country: Ireland" would be visible in the UI, but would be computed based on the contents of the knowledge base. The same applies to age and many other properties, that are useful for 'beginners', but can be computed from the other properties and rules expressed in the ontology.

Cheers,
Aleksander