### 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)

_enable_attributes(range_start, false);
			if (pb->color_disabled && pb->color != Color(1.0, 1.0, 1.0, 1.0)) {
				glVertexAttrib4f(RS::ARRAY_COLOR, pb->color.r, pb->color.g, pb->color.b, pb->color.a);
			}
			if (pb->index_buffer != 0) {
				glDrawElementsInstanced(prim[polygon->primitive], pb->count, GL_UNSIGNED_INT, nullptr, 1);
			} else {
				glDrawArraysInstanced(prim[polygon->primitive], 0, pb->count, 1);
			}
			glBindVertexArray(0);
			if (pb->color_disabled && pb->color != Color(1.0, 1.0, 1.0, 1.0)) {
				
				glVertexAttrib4f(RS::ARRAY_COLOR, 1.0, 1.0, 1.0, 1.0);
			}
		} break;
		case Item::Command::TYPE_PRIMITIVE: {
			glBindVertexArray(data.canvas_quad_array);
			glBindBuffer(GL_ARRAY_BUFFER, state.canvas_instance_data_buffers[state.current_data_buffer_index].instance_buffers[state.canvas_instance_batches[p_index].instance_buffer_index]);
			uint32_t range_start = state.canvas_instance_batches[p_index].start * sizeof(InstanceData);
			_enable_attributes(range_start, true);
			const GLenum primitive[5] = { GL_POINTS, GL_POINTS, GL_LINES, GL_TRIANGLES, GL_TRIANGLES };
			int instance_count = state.canvas_instance_batches[p_index].instance_count;
			ERR_FAIL_COND(instance_count <= 0);
			if (instance_count >= 1) {
				glDrawArraysInstanced(primitive[state.canvas_instance_batches[p_index].primitive_points], 0, state.canvas_instance_batches[p_index].primitive_points, instance_count);
			}
		} break;
		case Item::Command::TYPE_MESH:
		case Item::Command::TYPE_MULTIMESH:
		case Item::Command::TYPE_PARTICLES: {