Yes they should work in the other rims since they came off another 4Runner. You'll have to get the sensors swapped into the other set of rims. You mentioned that you only got 4 Limited rims. If you ever got a flat, you might have to use the wheel that may be slightly off sized than the other 4 wheels.
Note: Be aware that your spare tire also has a tire pressure sensor.
Also, as far as I am aware the TPMS is not tuned into your brakes. It looks at tire pressure to let you know your tire is low. We have an active system. Some other vehicles have a passive system that uses the ABS sensors. When a tire is deflated, it spins slower than a correctly inflated tire. The ABS picks up that it is spinning slower and notifies you that a tire is low on air.