Is the "requirement" in the maintenance guide for tire rotation every 6 months/5000 miles a TOYOTA vehicle warranty requirement or a TIRE manufacturer's requirement? Will failure to rotate tires INVALIDATE the TOYOTA VEHICLE warranty?
Should not affect the vehicle warrantee (other than perhaps road service if the flat was due to a worn tire?), but the tire warrantee will be. Your tire life will be shortened without rotation. Most tires do not have a mileage warrantee, but instead "for the life of the tread."
Rotating your tires every 5k is just good tire maintenance. I doubt that Toyota could prove one way or another if your tires had been rotated or not. If you miss a rotation and do it at 10k, not a big deal.
I'm kind of ambivilant about rotating the factory tires because they are nothing to get excited about. I have rotated them once so far. On top of that dealers actually charge to rotate the tires, but once you get better tires you purchase,the rotations are generally part of the service you get from the tire dealer you are buying from. It is garbage that dealers charge to rotate tires, they are the ones that sold you the tires with the car.
Fronts wear out much faster than rears, especially at the outer edges if you drive fast on corners. Higher pressures help this a bit. Rotating front/rear maximizes the tread life by spreading the wear to 4 tires from 2. If yours are wearing evenly, you could probably stretch it to 10K miles. Be sure your alignment is good also.