### 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)

if (instance_uses_color || instance_uses_custom_data) {
						glEnableVertexAttribArray(5);
						glVertexAttribIPointer(5, 4, GL_UNSIGNED_INT, instance_stride * sizeof(float), CAST_INT_TO_UCHAR_PTR(instance_color_offset * sizeof(float)));
						glVertexAttribDivisor(5, 1);
					}
				}
				GLenum primitive_gl = prim[int(primitive)];
				if (use_index_buffer) {
					glDrawElementsInstanced(primitive_gl, mesh_storage->mesh_surface_get_vertices_drawn_count(surface), mesh_storage->mesh_surface_get_index_type(surface), 0, instance_count);
				} else {
					glDrawArraysInstanced(primitive_gl, 0, mesh_storage->mesh_surface_get_vertices_drawn_count(surface), instance_count);
				}
				glBindBuffer(GL_ARRAY_BUFFER, 0);
				glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, 0);
				if (use_instancing) {
					glDisableVertexAttribArray(5);
					glDisableVertexAttribArray(6);
					glDisableVertexAttribArray(7);
					glDisableVertexAttribArray(8);
				}
			}
		} break;
		case Item::Command::TYPE_TRANSFORM:
		case Item::Command::TYPE_CLIP_IGNORE:
		case Item::Command::TYPE_ANIMATION_SLICE: {
			
		} break;
	}
}
void RasterizerCanvasGLES3::_add_to_batch(uint32_t &r_index, bool &r_batch_broken) {