In The Legend Reborn, the weapons of the Glatorian were said to have an organic origin, to explain why the Mask of Life was able to alter them. The weapons, however, look like regular metal weapons, and so one fan's theory that Spherus Magna inhabitants had metallic bones was canonized. That most weapons would be forged from bone-metal makes a lot of sense when one realizes that shortly (relative to the thousands of years the story spans) before the Core War, the Iron Tribe, which supplied the other tribes with mined metal, was destroyed. With their world's foremost miners gone, the inhabitants would need to turn to another source of metal to arm themselves.
The Golden Armor from Journey's End is a blatant Deus ex Machina, no doubt about that, however it isn't the first time we've seen something with that power. The Golden Kanohi - introduced at the end of the Quest for the Masks arc, and used throughout the Bohrok Saga - were also capable of absorbing and combining powers into one tool.
The title of the series itself. "BIONICLE" means "biological chronicle". The vast majority of the characters and creatures throughout the series' run had all lived inside what appears to be a giant robot with a whole world inside it. The story is a chronicle of this robot's biology.
Alternate Universes are by default seen as less important to the main one, simply because in the BIONICLE fiction, they are merely side-branches of the main timeline. This means that no matter what atrocities may happen in those worlds, these are simply glossed over. For example, just think of Tridax: he kidnapped and forcibly corrupted a whole bunch of Takanuvas from various other dimensions, who were then either killed during the Destiny War or freed and then killed by the Alternate Teridax. Not only does this mean that the main universe characters condoned killing originally innocent Toa who only turned evil due to a crazed villain, but also that all those other universes have been robbed of their only Toa of Light, one of their most powerful heroes. But since they aren't the main universe, they don't seem to matter.
Boxor are made of Bohrok. And what are Bohrok? Former Av-Matoran. The Matoran used the parts of their 'un'dead brothers and sisters to fight against more of their 'un'dead brothers and sisters!