Oh, a judge rules question! Here's where we'd come down on it:
At the moment, there seems to be a misunderstanding of the rules built into the question (which means we should perhaps clarify on the submission requirements page). When we look for source in an arrangement (rule of thumb: at least 50% of the arrangement should reference the source), what we're looking for is the arrangement/ReMix to be referencing the source at least 50% of the time, not for the arrangement to reference at least 50% of the source. As long as it's identifiable as the source, one could theoretically make a remix that only references 25% (or even less) of the source and it would still qualify for OCR as long as the arrangement was referencing that source for a significant period of time (again, rule of thumb is 50% of the arrangement). It would be odd leaving out so much source (and people might get upset that their favorite parts were left out!), but that's not technically a Judging requirement.
Concerning your actual question, though, which source would we give credit to in this case? Very likely, in this case it would be whichever source the artist claims to have been arranging since it's not technically wrong to call the arrangement a "Link Between Worlds" arrangement, even when it's similar/identical to the Link to the Past source. In the past I've sourced Dracula X's Stage 6 track for my submission (which is itself an arrangement of the Castlevania 3 "Beginnings" track), so I have some personal experience on that front to help come up with that conclusion. Forcing people to use "official" versions of the source would, I imagine, cause the staff quite a bit of headache figuring out which source is the "actual" source, which otherwise we'll only do if the VG track is in fact an arrangment of a well known non-VG track (like, say, one of Michael Jackson's songs used in his "Moonwalker" game - can't ReMix "Smooth Criminal" just because it's in his game, folks!).
Hopefully that answers your question!