I have to wonder if the people assembling the box set didn't know about the 2001 DVD-A at all, given the "2012" designation for the three 5.1 tracks included.
Often at big companies the staff turnover is such that there's a kind of "institutional memory loss" because there's no one there that was working there 10 years previously, let alone 20 to untangle the complicated provenance of the mixes and say 'well actually, the three bonus 5.1 mixes on the 2012 DVD-V come from the 2003 UK SACD, and those were sourced from the 2001 US DVD-A.'
I know it seems obvious to us here who live and breathe this stuff, but for the people whose day job it is to put these things together, it's not always obvious - for all they knew these were bonus remixes done in 2012. There's also the complicating factor of two huge monolithic companies at play - it seems like outside of the 2001 DVD-A, all of these sets (2003 SACD, 2012 box set, this new set) have been assembled by Deep Purple's UK label (EMI or whatever subsidiary of UMG it is) who have the distribution rights for Deep Purple outside of North America where Warner does that job. The UK label may either not have knowledge of the full 2001 US 5.1 mix, or maybe negotiated digital rights in perpetuity to the three 5.1 bonus mixes for the 2003 SACD and don't want to open up that Pandora's box again. Or maybe they just feel like those three 5.1 mixes have unique mix-related value that the other tracks don't have, though even if that is the case it seems baffling not to include the entire 5.1 mix.
When this comes out, it'll be interesting to see what the digital provenance (via spectral analysis) of the 5.1 tracks, because I think it'll give some clue as to which of the above is correct. If they're straight 24/96 PCM (from the DVD-A or equivalent digital master) then I think the answer is "these are the only tracks we wanted to include" but if they look like they've been transcoded multiple times (ie. 24/96 PCM -> DSD (for the 2003 SACD) -> lossy Dolby Digital (for the 2012 DVD-V) -> back to lossless PCM for the new box set BluRay) then the answer is most likely "we used what we had and didn't know there was more".
Often at big companies the staff turnover is such that there's a kind of "institutional memory loss" because there's no one there that was working there 10 years previously, let alone 20 to untangle the complicated provenance of the mixes and say 'well actually, the three bonus 5.1 mixes on the 2012 DVD-V come from the 2003 UK SACD, and those were sourced from the 2001 US DVD-A.'
I know it seems obvious to us here who live and breathe this stuff, but for the people whose day job it is to put these things together, it's not always obvious - for all they knew these were bonus remixes done in 2012. There's also the complicating factor of two huge monolithic companies at play - it seems like outside of the 2001 DVD-A, all of these sets (2003 SACD, 2012 box set, this new set) have been assembled by Deep Purple's UK label (EMI or whatever subsidiary of UMG it is) who have the distribution rights for Deep Purple outside of North America where Warner does that job. The UK label may either not have knowledge of the full 2001 US 5.1 mix, or maybe negotiated digital rights in perpetuity to the three 5.1 bonus mixes for the 2003 SACD and don't want to open up that Pandora's box again. Or maybe they just feel like those three 5.1 mixes have unique mix-related value that the other tracks don't have, though even if that is the case it seems baffling not to include the entire 5.1 mix.
When this comes out, it'll be interesting to see what the digital provenance (via spectral analysis) of the 5.1 tracks, because I think it'll give some clue as to which of the above is correct. If they're straight 24/96 PCM (from the DVD-A or equivalent digital master) then I think the answer is "these are the only tracks we wanted to include" but if they look like they've been transcoded multiple times (ie. 24/96 PCM -> DSD (for the 2003 SACD) -> lossy Dolby Digital (for the 2012 DVD-V) -> back to lossless PCM for the new box set BluRay) then the answer is most likely "we used what we had and didn't know there was more".