Shinju Was
absorbing all chakra. It absorbed naruto's Kyuubi Chakra, His own Chakra, and his Sage chakra. It's far fetched to assume it also absorbed a chakra based seal ? A seal that juubito was able to get rid of?
I think tobirama was in the middle because minato had 1 arm. Either way, tobirama would have to touch hiruzen for minato to get the job done. If minato touched hiruzen, then tobirama wouldhave to touch hiruzen and hiruzen would be in the center. That doesn't mean Hiruzen performed the jutsu. Furthermore, Tobirama shouting let's go hints more to the fact that minato was the one porting because tobirama gave a heads up. If tobirama was doing the hirashin, He could've simply 'Touch and Go' like he usually did.
As to the Kunai bit.
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to that position on the rock where sasuke was standing, while the kunai lay far away near Kiba. Infact, it's already been established that minato can teleport a radius around the kunai, yet it's hard to believe that he can get back to that spot, which he already teleported to before?
I hardly doubt tobirama could ever port without seals... Minato said FTG seals never disappear, and that's probably what tobirama was going to use when Hashirama told him to 'prepare hirashin' - A pre-existing Seal. The mere fact that Minato can't port without seals (he bettered tobirama's FTG) and kakashi stated that it was unbelieve that obito could port without seals leads us to believe that it was minato doing that teleporting at that time... After all, Throughout this battle, minato's been the one using FTG for defence, while tobirama used it for the offence.