If all 4 TPMS sensors are operational and transmitting air pressure readings that don't trigger the light, you should be fine running a 5-wheel rotation as long as you keep all 5 wheels on the vehicle. If you use the spare in the rotation and then leave one of the wheels with the sensor at home, then you'll get the light.
The only other caveat with this is that the sensors are designed to "sleep" to prevent wasted battery life. I'm not sure what conditions make the sensor sleep, though. If it is just any movement, then driving with a sensor on the spare should keep it active. If it requires rotational movement, then putting it underneath without such movement will throw up the light.
Why on the Limited? All 4runners come with a full-size spare with no TPMS. So, in theory it should affect all 4runners the same way. Other than that aspect, manufacturers generally account for normal wear in the 4WD/AWD calculations through the computer. They understand that a user may have 3 very old tires and then have a new spare put on as needed.