Has the possibility of the arrow splintering or being lodged in her skull been brought up yet? I'm no medical expert, but the area torn through Neji didn't have any bones, right? The skull's what, one of if not THE thickest bone in the human body? If the arrow makes it in, who's to say it makes it out? It could get stuck inside or even begin to splinter once breaking contact, like a 9MM bullet running havoc inside her head.
It'd prove for even more problematic regen if either happened, supposing Tsunade would be able to regenerate afterwards, was still alive, and supposing her brain recovered 100% to its prior state.