### 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)

}
			} break;
			case Item::Command::TYPE_MESH:
			case Item::Command::TYPE_MULTIMESH:
			case Item::Command::TYPE_PARTICLES: {
				
				_new_batch(r_batch_broken);
				Color modulate(1, 1, 1, 1);
				state.canvas_instance_batches[state.current_batch_index].shader_variant = CanvasShaderGLES3::MODE_ATTRIBUTES;
				if (c->type == Item::Command::TYPE_MESH) {
					const Item::CommandMesh *m = static_cast<const Item::CommandMesh *>(c);
					state.canvas_instance_batches[state.current_batch_index].tex = m->texture;
					_update_transform_2d_to_mat2x3(base_transform * draw_transform * m->transform, state.instance_data_array[r_index].world);
					modulate = m->modulate;
				} else if (c->type == Item::Command::TYPE_MULTIMESH) {
					const Item::CommandMultiMesh *mm = static_cast<const Item::CommandMultiMesh *>(c);
					state.canvas_instance_batches[state.current_batch_index].tex = mm->texture;
					state.canvas_instance_batches[state.current_batch_index].shader_variant = CanvasShaderGLES3::MODE_INSTANCED;
					if (GLES3::MeshStorage::get_singleton()->multimesh_uses_colors(mm->multimesh)) {
						state.instance_data_array[r_index].flags |= FLAGS_INSTANCING_HAS_COLORS;
					}
					if (GLES3::MeshStorage::get_singleton()->multimesh_uses_custom_data(mm->multimesh)) {
						state.instance_data_array[r_index].flags |= FLAGS_INSTANCING_HAS_CUSTOM_DATA;
					}
				} else if (c->type == Item::Command::TYPE_PARTICLES) {
					GLES3::ParticlesStorage *particles_storage = GLES3::ParticlesStorage::get_singleton();
					GLES3::TextureStorage *texture_storage = GLES3::TextureStorage::get_singleton();
					const Item::CommandParticles *pt = static_cast<const Item::CommandParticles *>(c);
					RID particles = pt->particles;
					state.canvas_instance_batches[state.current_batch_index].tex = pt->texture;