The two plugs are the same EXCEPT for the connectors on the end of the pigtail....one is male, one is female. If you install them reversed, then your reverse lights will come on when you shift into 5th and the EGR will be over-ridden when you shift into reverse.....so you need to make sure you have them installed correctly (the reverse one is the front one (closer to engine), BTW).
Even the 86 samurai trannys had the rubber plug....so I don't think it was something that was engineered out of the tranny.....but I have no idea what the purpose of having a hole there in the first place would be.