You may have misunderstood what I was referring to. Here the assigned TestReference object has its property values saved to tscn and used to initialize a newly created object when the project is run. It ALSO saves all of the values of the Node that the TestReference is pointing to. I've expanded the test a little bit:
class_name TestNode
extends Node
@export var _res_1:TestResource
@export var _res_2:TestResource
@export var _node_ref:Node
class_name TestResource
extends Resource
@export var target:Node


and the resulting .tscn from all of that
[gd_scene load_steps=5 format=3 uid="uid://bkf16rjaesl84"]
[ext_resource type="Script" path="res://test_node.gd" id="1_kmmcv"]
[ext_resource type="Script" path="res://test_resource.gd" id="2_ups2k"]
[ext_resource type="Resource" uid="uid://f7nlj7i4unbb" path="res://test_resource.tres" id="3_lnf6o"]
[sub_resource type="Resource" id="Resource_a7l4x"]
script = ExtResource("2_ups2k")
target = Object(StaticBody2D,"_import_path":NodePath(""),"unique_name_in_owner":false,"process_mode":0,"process_priority":0,"process_physics_priority":0,"process_thread_group":0,"editor_description":"","visible":true,"modulate":Color(1, 1, 1, 1),"self_modulate":Color(1, 1, 1, 1),"show_behind_parent":false,"top_level":false,"light_mask":1,"visibility_layer":1,"z_index":0,"z_as_relative":true,"y_sort_enabled":false,"texture_filter":0,"texture_repeat":0,"material":null,"use_parent_material":false,"position":Vector2(0, 0),"rotation":0.0,"scale":Vector2(1, 1),"skew":0.0,"disable_mode":0,"collision_layer":1,"collision_mask":1,"collision_priority":1.0,"input_pickable":false,"physics_material_override":null,"constant_linear_velocity":Vector2(0, 0),"constant_angular_velocity":0.0,"script":null)
[node name="Node2D" type="Node2D" node_paths=PackedStringArray("_node_ref")]
script = ExtResource("1_kmmcv")
_res_1 = SubResource("Resource_a7l4x")
_res_2 = ExtResource("3_lnf6o")
_node_ref = NodePath("Node2D/Node2D/StaticBody2D")
[node name="Node2D" type="Node2D" parent="."]
[node name="StaticBody2D" type="StaticBody2D" parent="Node2D"]
[node name="Node2D" type="Node2D" parent="Node2D"]
[node name="StaticBody2D" type="StaticBody2D" parent="Node2D/Node2D"]
I assigned the same deeply nested StaticBody2D to both the TestNode and the TestResource which lives inside the .tscn.
You can see that the TestResource sub_resource does not have a path to the StaticBody2D at all. It has an entire copy of the node I assigned to it.
The TestNode node, on the other hand, merely contains a NodePath pointing to the correct path of the StaticBody in the scene which I assigned to it.
Does that then make more sense what I'm trying to say? 😂 I don't always choose the correct or best terminology...