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.
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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.