### Godot version

4.1.1-stable

### System information

Windows 10

### Issue description

When the project loads in editor, all the settings defined in project settings will be loaded over the default values, but when running the game nearly 95% of them will be ignored resulting in just loading the default settings.

here it's just loading only 4 variables from project setting and i have added the fifth in this pull request https://github.com/godotengine/godot/pull/80151
![image](https://github.com/godotengine/godot/assets/53877170/926168a6-e6d3-4983-b59d-7fd202db681d)

GLES3::MeshStorage *mesh_storage = GLES3::MeshStorage::get_singleton();
			GLES3::ParticlesStorage *particles_storage = GLES3::ParticlesStorage::get_singleton();
			RID mesh;
			RID mesh_instance;
			uint32_t instance_count = 1;
			GLuint instance_buffer = 0;
			uint32_t instance_stride = 0;
			uint32_t instance_color_offset = 0;
			bool instance_uses_color = false;
			bool instance_uses_custom_data = false;
			bool use_instancing = false;
			if (state.canvas_instance_batches[p_index].command_type == Item::Command::TYPE_MESH) {
				const Item::CommandMesh *m = static_cast<const Item::CommandMesh *>(state.canvas_instance_batches[p_index].command);
				mesh = m->mesh;
				mesh_instance = m->mesh_instance;
			} else if (state.canvas_instance_batches[p_index].command_type == Item::Command::TYPE_MULTIMESH) {
				const Item::CommandMultiMesh *mm = static_cast<const Item::CommandMultiMesh *>(state.canvas_instance_batches[p_index].command);
				RID multimesh = mm->multimesh;
				mesh = mesh_storage->multimesh_get_mesh(multimesh);
				if (mesh_storage->multimesh_get_transform_format(multimesh) != RS::MULTIMESH_TRANSFORM_2D) {
					break;
				}
				instance_count = mesh_storage->multimesh_get_instances_to_draw(multimesh);
				if (instance_count == 0) {
					break;
				}
				instance_buffer = mesh_storage->multimesh_get_gl_buffer(multimesh);
				instance_stride = mesh_storage->multimesh_get_stride(multimesh);
				instance_color_offset = mesh_storage->multimesh_get_color_offset(multimesh);
				instance_uses_color = mesh_storage->multimesh_uses_colors(multimesh);