Part of Nagato's purpose was to eventually use Rinnei Tensei to kill himself in order to resurrect Madara.
Mmmm, no. Rinne Tensei only killed him because he didn't have enough chakra.
Konan confirmed this after talking to Naruto.
Nagato actually used Rinne Tensei and stayed alive. And a lot of times. He kept reviving his tenzos all the time.
So, to sum up, it's impossible that the reason Madara didn't put a seal on him was because he couldn't have used Rinne Tensei on Madara. He could have, because it wouldn't have killed him. So there was no reason not to put a seal on him in first place.