@Sam Bee I'm inclined to agree. There would seem to be no conceivable reason for HMRC to require the provision of individual locators.
My hunch - wrongly or rightly - is that the PNR data simply happened to be included along with other information which was necessary for annual tax returns - and that it was easier to supply it with than to 'separate it out'.
But the real concern IMO is that HMRC actually had the interest/time to identify the fact that two identical PNR's had been quoted within a seven year period. It could perhaps explain why some of the very largest global businesses, with sizeable UK-based activity, are - shall we say - the subject of much media comment where the payment of corporation tax is concerned. A matter of priorities, so to speak....
EDIT - this post crossed with your latest CWS.