I finally re-found the discussion I was reading years ago!
https://zota.org/2008/02/07/donkey-controversy/In the comments on this article there is an RTM reply, where he quotes an email from Greg Erway. In reference to Wiebe's DK and DK Junior records (for which Wiebe used a DDK board) Greg says:
"I do remember a discussion about the DKJr. score being reclassified too and that a decision was made (not sure who the group was that made the decision but I was not part of it) to not reclassify the DK Jr. score. The fact is, Double Donkey Kong is made out of an original DK Jr. boardset. There is a higher likelyhood of differences between DK Jr. on a unmodified board and a DDK board due to that fact. As much has been claimed for DK on a DK board and DK on a DDK board however I believe someone determined there was different timing in reguards to the timer (and how long you can live at 000 before a death)."I don't have access to a DDK for testing, but this would probably be pretty easy to test. (I believe DDK is emulated in MAME now, for what that's worth.)
At any rate, in all the years since this brouhaha, and despite suspicions about "likelihood of differences", nobody has conclusively (or even tentatively) demonstrated any disparity between DK running on a TKG board and DK running on a DJR board. IMO, since the hardware is near-identical, there's no reason to think that there would be a difference.
As far as I'm concerned, after all the remixing and <snek>ing John K. has proven to be an expert on DK on both the hardware and software level, so I would defer to his opinion on this. If he says "easy accept", then so do I!