Hmmm...
Basically you're asking whether the Flying Thunder-God Technique provides travel across a dimensional shift, in which case I doubt. Though a space time Ninjutsu, it thus far seems to operate only within the dimension of the user teleporting him from point A to B without traversing the space in between. There is a reason as to why Obito decided to get rid of Minato using Kamui, though the velocity Thunder-God technique's succeeds Kamui's warping ability which resulted in Minato's escape. Alternately, if Minato could teleport across dimensions I'm sure he would have opted for that during the kyuubi's attack to save his family as well as the village.