Sigh and you missed the difference.
Walling off Kyuubi's chakra completely blocks Kyuubi from coming out and its pretty patheticly easy to do.
Orochimaru did it with a 5 element seal and completely screwed up Naruto's ability to manipulate chakra.
Kabuto did it with medical ninjutsu almost killing Naruto.
Jiraiya made a seal that could do it and anyone could use it, but it only worked if he didn't hit 3 tails (Which should be a pretty strong indicator that at 3 tails its more Kyuubi then Naruto)
When Yamato did it he did it effortlessly and it was incredibly effective and did not strain Yamato in any appreciatable way.
What Yamato was doing during the Fuuton: Rasenshuriken training was acting as a filter for Naruto he was supressing Kyuubi's will while allowing Naruto to still use Kyuubi's chakra. That required Yamato's full concentration, lots of chakra and massive effort on his part.
The reason why its so easy is essentially your blocking off the chakra from entering Naruto's chakra system. Thats easy to do and Kyuubi has no way to affect Naruto. It also screws up Naruto's ability to control chakra, prevents him from healing. Anyone and thier mother could do this if they know sealing techniques. How ever if Naruto gets pissed off enough unless you like severed the connection physically which is what Kabuto did Kyuubi will blow right past it or it just won't work anymore like Jiraiya's seal only worked up to two tails...