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Is this file somewhat "incorrect" ?
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File definition of discussed settings are correct, what is inside is another question, but there is quite common combination for it (sRGB->YUV with BT.601 conversion matrix).
Recommendations BT.601 and BT.709 use same definition for transfer characteristics, h.262 and h.264 don't have different coding for it, they both define only BT.709. Also this coding is more than similar to sRGB definition. So, BT.709 for transfer characteristics is absolutely correct.
Recommendation BT.601 defines 2 possibilities for color primaries. One (for PAL) is similar to Recommendation ITU-R BT.470-2 System B, G. Another one (NTSC) is similar to SMPTE 240M (1987). Strictly said they are not compatible with sRGB, that is computer can't correctly show these colors. So in digital world old color primaries are not being widely used. As standards h.262 and h.264 allow separate coding for color matrix and color primaries it's ok to mix values from different origins. So, setting color primaries to BT.709 is valid, even though it might be incorrect for some weird sources captured in original BT.601 color primaries (but it's the responsibility of capturer to set color primaries correctly in this case).
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Does this mean that BT.601 was used to derive luma and chroma values from the sensor's RGB data, but that BT.709 must be used to convert back YUV data to RGB ?
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Nope, BT.601 color matrix must be used to convert YUV data back to RGB, but this RGB will be BT.709-compatible RGB.
For computer processing/presentation it will end up in sRGB in fact instead of BT.709 RGB. Strictly said they are different, but difference was judged to be non-significant during sRGB development.