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I thought manstopper rounds were hollow points, not slug rounds? Was I wrong? Anyways, on to the question.

Boring non-fluff answer: game balance.

Possible fluff explanations: If it is due to ammunition (solid slug vs shot) there are several reasons a guardsman may choose to use different ammunition than a SM, and it would likely be a combination of them.

First, you have a better chance of hitting your target. A Space Marine, with their decades of experience and super human reflexes may not need that as much as raw power, while the guard may prefer increased chances of hitting to stopping power.

Second, you have to take into account the intended target. There is a reason we largely stopped using 30-06 ammo in war, but continue to use it when hunting big game. It was overkill for humans. Likewise, the IG typically faces humans, and thus scatter shot is typically sufficient, while a SM will often be facing orks, daemons, tyranids, etc.

Third, you already mentioned: SM just use bigger weapons. I really don't understand your counter to this point. Ok, in Necromunda humans can fire manstopper rounds. That doesn't mean the SM manstopper round is the same thing as a regular humans, or that a SM shotgun is the same size as a regular one.

Those are my thoughts. I don't think there is a hard answer.