My real-time encoder isn't using the punchthrough mode bit or the transparent mode bits, either. Even with fully opaque textures, cleverly using these mode bits would reduce error. But I would then have to do expensive error calculations during transcoding.
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It seems like not having the same number of bits for each channel is just asking for the hue to get shifted around whereas saturation and luminance changes are less noticeable.
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The blueish hue shift is quite noticeable on really low saturation content.
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Back in my scanner driver life I noticed that image processing worked a lot better in HSL and a lot faster in RGB, so I put in an option to do speed or quality.
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Found a potential solution for better PVRTC quality: Precompute the best mode bits to use for all possible (5,5,5) ETC1S block colors and 3-bit intensity table indices. Just a few bits per entry so the table isn't too large. (I'm transcoding from ETC1S encoded pixels, not RGB)
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