Now that someone’s posted I can make a new post without getting yelled at for double posting. Here’s the silver-as-mutation theory.
In a similar vein to the above theory which states that rubber parts represent organic matter, I propose that silver parts represent a variety of things, chief among them mutated parts, but in general things that are not natural to a being.
So what do I mean by that? Silver made its big premiere to the BIONICLE theme in 2002, with the Toa Nuva. It is true that silver parts appeared in sets before this - namely, the Rahi sets, where silver panels and flex tubes appeared on the Muaka & Kane-Ra and Tarakava sets. However, the main introduction of silver to the theme was the Toa Nuva. The Toa Nuva, at their base, are extremely similar to the Toa Mata, the Toa that they began life as, but they are augmented with silver pieces. Remove their silver armor, and they suddenly look much more like their 2001 selves. Additionally, their weapons, which were once their primary colors, are now silver as well to match. The Nuva were followed by the Bohrok-Kal, themselves augmented versions of prior sets in a similar way, also featuring silver as a major component of their color schemes.
In the lore, the Toa Nuva and Bohrok-Kal have something more in common - they were both created by exposure to a mutagenic substance. I propose, then, that this is where the association between silver and mutation starts. The Toa Mata start out with no silver parts, get mutated, and gain silver parts in the process. The Bohrok start out with no silver parts, get mutated, and gain silver parts in the process.
However, given later developments, mutation can’t be the only source of silver on figures. The Toa Metru were not mutated, but they wielded silver tools - my proposal, then, is just that these tools were not created for the Toa Metru in the same way that the Toa Mata’s tools were created for them, and instead these are just simply generic Toa tools. Silver as a color for a “generic” item shows up elsewhere, with the Rahkshi staves and Kolhii sticks of 2003 also being molded in silver to indicate that they are not essential to their holder like the tools of the Toa Mata.
If we analyze some of the other uses of silver on non-Rahi characters in 2004 (because the Nivawk uses silver pieces too), we can see the same pattern take place. Krekka uses his silver as body armor - it covers his pecs and back, and his boots are mainly silver. Nidhiki is notable for being mutated - large parts of his body, including his Vahki-like face, his claws, his torso, and his legs, are silver. The Vahki staves and launchers are all silver, indicating perhaps that they can be removed, and of course the Matoran’s disk launchers are silver because they are not part of their bodies like the '01 Matoran.
The next time we get primarily-silver Toa is in 2005, where the Toa Hordika have been massively mutated as part of their form change. Their bodies are primarily silver in the same way as the Toa Nuva. Other uses of the color from that year include Sidorak, who uses it sparingly, and Roodaka, who does seem to use it for armor (note her chest and boots).
This pattern continues for more or less the entire series. Other good, isolated examples include Ehlek’s claws (which we know are not part of his body), Hydraxon’s helmet, and basically every weapon and Toa tool through the end of the series. The only time that silver seems to be used to represent something essential to a character/figure is on Rahi, where creatures like Spinax, Gadunka, Muaka, Kane-Ra, Visorak, Tarakava, Hydruka, and Klakk all use silver to represent parts of the body that couldn’t logically be attachments or mutations.
TL;DR: Silver pieces used on non-Rahi characters represent mutated parts, or parts that are removable, such as armor and tools.