Oh boy, sorry to resurrect such an old topic, but I've been trying to make some TFH edits too.
It looks like you used "extract" with
ctpktool, because when you use
-r to extract the raw images, they're something else. I think they might be ETC1(A4) because the colour compression looks similar, and each 64x64 image is a standard size, 4 KB.
Tri Force Heroes uses ETC1(A4) textures in many the
.bch models, but I'm not sure how .bch viewers can tell what the compression is, or how they extract them.
[EDIT]
When ctpktool is extracting the images, the list shows they are
.tga files. But they aren't the same as the common "TARGA" .tga format, so maybe it's a different format that Nintendo uses?
[EDIT]
Looking at the .xml files that ctpktool produces, these images have a "format" number of 13 (0xD). I've seen a few scripts that refer to a format like this. smealum's
bch2png (Python) indicates that 13 is ETC1(A4).
[EDIT]
Sorry for all the edits. I think this will help!
https://github.com/Cruel/3dstex