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It was originally implied that the reason protodermis was so special was because it was a "living" metal and all Bionicle creatures were made of it, making them basically living robots. It was almost called "biodermis", but that name was trademarked by another company already; the original name likely would have made the implication clearer. The Onu-Koro chapter of the MNOG was originally going to have a "biodermis smith" who built Rahi from biodermis sourced from the mines. You can still see evidence of this in the finished game in that the Matoran mining equipment consists of tool/Rahi hybrids. The "cyborg" angle was only really formalized in 2003 when they switched gears for Mask of Light for some reason.
I'd say that "living robot" is the way to go for animations because A: it's the most unique option and B: the "technic-ness" of the Bionicle system in 2001-2 gave creations a pleasently "lego-y" quality, which somehow combines the abstract clunkiness of mainline System building with sleek turn-of-the-millenium modernity seamlessly. The sets adhered to the "living robot" paradigm for the entirety of G1 despite the movies being the "canon" version. The Advance and Templar animations using this paradigm had a more "cinematic" quality than the movies anyway.
As for the masks, part of why the Advance and Templar animations are seen as being more faithful to the core concept of Bionicle than the Miramax films is because they kept the masks static, which made the characters seem more mysterious and alien. Of course, based on their personalities as written Bionicle characters seem pretty close to being human, but it's best to leave room for creative interpretation. Templar was able to give characters a wide range of personalites while maintaining an aloof tone and only having the characters express themselves through gestures and their eyes (and a few bits of anime iconography, though it's best not to go overboard with that).
