Ha! I knew naruto was going to learn the FTG since his shushin isn't all that great when u compare Raichus. It will be epic though.....
IMO, The FTG like all other T/S jutsu are based on the control of Yin and Yang based chakra. More likely Yin more then Yang probably.
Notice that basic summonings are done with blood plus the application of ones chakra.
I think that spiritual energy is at its most concentrated form in the blood as YIN base.
And that for T/S jutsu to do what they do, I believe spiritual energy must be capable of conducting and reacting to the users spiritual energy over any distance and isn't bound by space or time.
This also must apply to the spiritual energy of animals and other people through a blood contract which allows one to summon an animal or person despite not having the same spiritual energy.http://www.mangareader.net/93-97-19/...hapter-92.html
Spiritual energy in the form of minato's blood seal either on a flying kunai or Tag on a person or object is activated by minato focusing his own chakra, Which then transports minato to his Blood seal instantly through a dimensional door way instantly.
Basically, By focusing his chakra on his blood seal (kunai or tag), which has his spiritual energy in it, it can pick up on minatos chakra and activate, transporting him due to spiritual energies ability to conduct over any distance.
Thats my theory on The "Flying-Thunder-God-no-jutsu". And the majority of all other T/S jutsu as well.
Now its application to "that jutsu" for naruto to finish and use to beat madara as planned by Minato.
Minato figured out that Madara Uchiha being able to summon the Kyuubi, (a massive amount of spiritual/physical energy chakra beast) is due to madaras spiritual energy/YIN based chakra being the same as the kyuubis. (And Karin also Implies the power of sasukes MS and the kyuubis power are the same.)
SO, with naruto having the power of the kyuubis YIN powerful chakra which is the same as madaras YIN chakra as well... With same spiritual energy as madara in kyuubi form.... Naruto will be able to transport himself to madara at will!!!!
Naruto can just FTG to madara at will.
Note: The kyuubis wicked spiritual energy/YIN based chakra could allow naruto to FTG to anyone with wicked YIN based chakra, not just madara.