If Hisoka saw Chrollo's hand trying to punch him, he would have seen him trying to poke him with a needle. I concede the point about Chrollo's stealth abilities, but Muzan dealt with superior ones that involve multiple presence concealment talismans that give literal invisibility, implying he can detect someone with a lesser amount of talismans.
According to Hisoka, Chrolo needs one to two seconds in order ot create a puppet, and he will need more time to use Sun & Moon and Order Stamp. So people in an open space and not distrated by watching Hisoka in the arena will notice and panic due to a crazy guy creating corpses by touching people. UP1 said that his flesh sword will disintegrate if he tries to cut Gyomei's high-quality Nichirin chains, so Nichirin does have some durability negation. This means that Chrollo has no option but to get in melee range.
Furthermore, in order to use Order Stamp to issue a simple attack command, the puppets need to know who the person is and his location. So at best in order to not be shouting in viewing distance from Muzan, Chrollo would need to draw a picture of Muzan and show it to peoploe before he creates any puppets from them (he also can't teach people about Sun & Moon to ensure the puppets explode correctly). The corpse puppets did not demonstrate the ability to create and maintain new memories. This is extremely inefficient.
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Even if you define AoE differently, we can agree that Muzan can attack in a large radius and easily incapicate a group of puppets with one swing, and Muzan has demonstrated the ability to attack with eight tentacles simultaneously. Gon who had a much greater affinity to Emission due to being an Enhancer tried energy projection and it was rather weak. Chrollo doesn't have Ren feats to no-sell decently powerful attacks, and he would have one of the worst Nen affinities to due so because he is a Specialist.
If Black Voice doesn't use a physical phone then it can't be reconjured easily. Shalnark is afraid for his phone breaking if mishandled by others.
To summarize why Muzan wins:
- The puppet strategy is only effective in a combat arena setting, and is highly ineffective as a distraction here
- Creating clones is limited and has with severe disadvantages such as not being able to use additional abilities
- Chrollo has no choice but to get in melee range of Muzan, in which case he is likely to get at least scratched due to Muzan spamming several wide-range attacks at the same time, and getting scratched is enough for Chrollo to die. Chrollo has no way to ensure his victory or develop a 'safe strategy' nor can he win at a distance with puppets. Chrollo will run out of stamina faster since Muzan has higher stamina, reactive evolution, and can strengthen himself by further eating the corpse puppets