Displaying locations with identical coordinates together

Marking this as Support Request, as this clearly doesn't report any Bug,
but just a lack of awareness (or documentation, but still on a very specific use case).

If you have multiple entities with a geofield that store the exact same (lat & lng) coordinates.
it is pretty obvious that you would end up on a bunch of different location entities that share the exact same coordinates.
Clicking on the Geofield Map, without markeclustering & spiderfying, of course it will open only the Popup of the Marker that is at highest level (Z-Index), and only render - list the Entity that is linked to that Marker.

The proper way to accomplish your needs should be to extend your data model and split it into 2 entities:
- location(s) entities, that embed the Geofield (and eventually the same Address), with unique (don't ever duplicate)
- content(s) entity that have an entity reference field to a location (entity). Eventually you could create both the new Content and new Location at the same insert time, if the Location (Address) is not yet created.

With this data model, architecture you can then create a Geofield Map of your defined Locations (and may be filter only those that have at least one Content referring to ... ) and then make each Marker Popup list all the Contents that refer to that Location (such an embedded reverse View: list all the Contents that refer to this Location).

This is a common (and smart approach) and you could eventually have a look to the "Geo Entity" module for some inspiration (or even exact reference) on what kind of Location Entity you might create and rely to ...

Hope (and very confident) this helps and points you to the proper approach.