You are a bit confused...
In the first case, you really do have to kill the entire group of neutrals, even if by repeatedly attacking the last ones. That is, systematically killing all groups.
In the second case, only the unupgraded neutral units are killed, we flee, and the entire neutral group disappears from sight. Thus, in this case, the upgraded stacks are obtained "for free," and that is not good.
And the tactics end up being completely different, not identical, as you claim.
In principle, it seems illogical to me that carrying a neutral without penalty is allowed (and this is clearly a bug). Moreover, by using it, the player in the game suffers no material losses, unlike using the neutral elimination trick (here they do suffer material losses for it, see above). Nevertheless, this trick is banned. If we look at the big picture, then either both of these tricks should be allowed, or both of these bugs should be banned :)