What people need to understand is that just because Senjutsu is effective against Juubito doesn't mean he's super weak against it. It's just in comparison to ninjutsu which has absolutely no effect it's better.
Just because he broke out of the seal, doesn't mean the seal had no effect, it just means he was stronger than the seal. Naruto's rasengan on the other hand is an attack that caught him off guard so it had a better effect. Also we don't know how Obito will bounce back from this so it's too soon to jump to too many conclusions