It has to. Neji is targeting to stop the chakra pathway system, which is connected to vital organs. When he is in the expansion form, his skeletal system, organs, etc., has to grow with him, otherwise how would he be able to operate.
It is also very unlikely that Neji is even able to climb on Choji, considering he can jump/fly over mountains. Even if he manages to reach his foot, and proceeds to climb up towards his upper torso, it only takes one sweep of chojis hand to knock Neji off.
Again, Chojis enormous size comes into play here. A vacuum palm from such a far distance isn't going to do much against Choji.
Neji speed still fails in comparison to Chojis strength and power. The force of his stomp will most likely blow Neji away.
That is true, but really how long does it take for Choji to transition into BM or use his expansion jutsu... a few seconds a best. Unless the fight starts at a few feet away (Unlike every fight we have seen in Naruto) that isn't happening.