The nipple 'exception' is there to cover the ubiquitous 'Romex risers' all over America -- coming vertically up out of a panel. Whatever heat buildup induced by such a short run is cancelled by the 'naked' (sheathless) conductors within the panel.
Due to practice, and economics, such long nipples are not seen elsewhere in Romex installations.
NEMA standards limit Romex to 3 conductors plus a bare/ papered grounding/bonding conductor.
The NEC is just doing its part to make sure that no-one attempts to bore (hole saw?) oversized penetrations within wall studs. Yes, more, smaller, penetrations result in a stronger stud/ joist.
Anyone stuffing Romex beyond three cables per... is naughty.