The only examples I can think of:
Muschamp/Mack Brown at Texas. Muschamp ended up leaving and taking the FL job and never became TX head coach. This proves that the HC in waiting title doesn't mean much.
Jimbo Fisher/Bobby Bowden at FSU: Jimbo won a NC after Bowden retired, but the last few Bowden years were not good. Naming a HC in waiting basically is a death knell to the current coach since it undermines him and his authority. I wouldn't want to sacrifice Kelly's last few years (especially with how well ND is currently playing) just to keep Lea.
You may be referring to Riley at OU and Day at OSU. Both were promoted from within, but neither were ever named HC in waiting. If Kelly unexpectedly retires after this year, then Lea should be considered for a promotion like they were, but it doesn't mean you name him HC in waiting.
Also, Kelly will likely be the HC for at least another 2-3 years. That's a long time for Lea to wait. He may no longer be the hot name his is now at that time.