Regression: Embedded documents with same _id but different values are now treated as identical after version 9.0.8

[lucasDechenier]

Description

After upgrading from Mongoid 9.0.7 to 9.0.8, a breaking change occurred in how equality (==) is handled for embedded documents.

Previously, it was possible to store multiple embedded documents with the same _id but different values when a custom == method was defined.
Starting in version 9.0.8 (after the changes related to [MONGOID-4889](https://jira.mongodb.org/browse/MONGOID-4889) and [PR #6010](#6010)), Mongoid now treats embedded documents with the same _id as identical, ignoring any custom equality definitions.

This results in previous behavior no longer being possible.

---

Steps to Reproduce

module Documents
  class PropertyValue
    include Mongoid::Document
    embedded_in :document, class_name: 'Documents::Document'

    field :id, type: String
    field :value, type: Object

    def ==(other)
      id == other&.id && value == other&.value
    end
  end
end

doc = Documents::Document.new
doc.property_values << Documents::PropertyValue.new(id: "x", value: 1)
doc.property_values << Documents::PropertyValue.new(id: "x", value: 2)

puts doc.property_values.size

---

Expected Behavior

Both embedded documents should be present, because the == method defines equality based on both id and value.
In previous versions (up to 9.0.7), the output was:

2

---

Actual Behavior

Since version 9.0.8, the second embedded document replaces the first one.
The output is now:

1

Mongoid treats documents with the same _id as the same object, regardless of the custom == implementation.

---

Question

Is there any supported way to restore the previous behavior where custom equality logic (==) was respected for embedded documents?
If not, is this change intended to be permanent, and should applications now avoid relying on custom equality methods for embedded document uniqueness?

---

Environment

• Mongoid version: 9.0.8
• MongoDB version: 7.0.x
• Ruby version: 3.1.4
• Rails version: 8.0 / 8.1

[johnnyshields]

Possibly related to: #5982