Because Neji can't strike the Tenketsu if there's a thick layer of bone above them.
Its like holding a steel plate in front of your chest and then telling Neji: Yo dude... now strike the Tenketsu on my chest please.
kimimaro was hit by Lee,but it was because lee uses taijutsu. neji's attack can't win against kimimaro: gaara's techniques were useless and gaara is stronger than neji.
not even almost look at the last panel, its like the blade didnt do any shit against his bones
^It shows that its at least very chakra resistant, because otherwise the blade would have gone right through it.
Kubikiribōchō is one of the seven legendary swords of the mist, so one can assume its made of the highest quality steel, yet it was basically like butter against a chakra stream weapon. Which in turn means Kimis bones are so dense that they can't be penetrated even by chakra.
Not sure a chakra blade and gentle fist can be counted as the same thing. Gentle fist has not impact power whatsoever so to speak, it simply sends chakra into the body. A chakra blade does not send chakra into the body, it works inherently differently. The chakra in the chakra blade merely enhances the edge of the blade, it makes it sharper, harder and maybe heavier so to speak. The comparison is pointless at best IMO.
As for how the beheading sword would work, I doubt it is nearly as simple as people make it out to be. For one thing, it is a pretty damn big and heavy sword. Even if it does not cut kimimaru it is bound to hurt due due to the sheer weight behind it. For another, breaking it is perhaps not the best move for kimimaru. All the user would need is a dent to kimimaru's bone armor and have him bleed to start sucking out his blood and repair the sword. Even if just a little blood is drained it is something that can be build up in a long battle.
More importantly, the beheading sword was NOT cut by a chakra infused weapon. The beheading sword was cut by a blade infused with lightning chakra which could be extremely important. As we know lightning enhanced the vibrations and cutting power of the weapons to a great degree. I would think the cutting power of a sword with lightning chakra is significantly higher than the cutting power of a sword with regular chakra. We don't know how kimimaru's bones would ultimately hold against the beheading sword. Kimimaru is bound to be resistant but IMO there are plenty of things that could be done to work around that.