Having looked at and ran each version of the game, there is quite a bit of variance that can happen on the border raid stage despite the movement speed changes and bottle values. As researched in the TAS notes for this game https://tasvideos.org/7725S we see that the bottle locations are determined by the frame you shoot them on, so it's possible for someone to have amazing luck here and get a really low border raid time on any version of the game. My best time on the border raid stage over all the versions of the game is on the blue label revision. The railway stage will be slower on the US versions, although you can push the carriage to speed things up a bit and due to the slower speed of the stage that strategy is much safer. It seems like based on my splits that you lose about 30 to 40 seconds on the railway stage vs the Famicom version.

I don't have much of an opinion on splitting the board besides the lack of players, I'll run each version if the board is split so it doesn't matter much to me.