This is pulled directly from the SpeedDemosArchive KnowledgeBase, which I feel deserves to be distinctly posted here in the forum. My own thoughts on the matter are presented after.

"There are several differences between the ntsc-u and ntsc-j versions. The difficulty of this game (without a walkthrough) is absolutely ludicrous. My guess is that someone tried to tone down the difficulty a notch or two before releasing the game in the US (it's still ridiculous though). Anyways, some items have been moved around, some blocks take more jumps to destroy in the Japanese version etc. For the best ending category, this means that it's meaningless to compare the two versions. For the normal ending, you have to make five block breaking jumps more in the j-version. These extra jumps also mean that an extra mighty coin is needed in the j-version. This equals roughly an additional 3 seconds or so (depending on how fast one is to break blocks). On the other hand, there is a chest in round 17 (room 17-2 to be more exact) that is visible in the j-version but not in the u-version. That room is roughly 1 second faster on the j-version. So overall, the u-version has a few seconds advantage over the j-version, but one should probably not compare the two versions down to the second."

Although the difference in time seems negligible I feel this is enough to cause runners to alter their approach to each version of the game, thereby necessitating a split in the NES & Japan releases. From what I understand there is a possibility that the Europe releases have even more variables so this is being further explored after the NES/Japan category split is finished.