So the cluster is a really messed up experiment, nobody will argue that. Homeworld took the shards of dead Crystal Gem warriors and smashed them together in an attempt at a super fusion. Garnet was upset that Homeworld used fusion in that way, understandably. But what if, unbeknownst to her, Garnet was actually the catalyst that set off the cluster experiments?
What if Homeworld saw how much stronger she was than fusions with the same gem? After all, 3 rubies fused together is just a larger ruby. Garnet actually gains powers, such as electricity, when fused. Not only that, but she seems to be much bigger and stronger than 3 rubies combined could ever be. So what if Homeworld tried to replicate that, by fusing gem shards together, in an attempt to make super soldiers?