All Japanese promotions are not done by JYP but by their reps in Japan. That's Warner Music for Twice and Sony for NiziU. I don't think JYP really care if Twice or NiziU is bigger. They just want ALL the groups to do good in Japan as they make more sales and money. The fact NiziU became so big was not expected as any fan who watched from the very beginning can testify. So the fact they have done better than Twice (recently) is not a planned action of JYP.
The thing with Sony is that they are doing a phenomenal job of promoting them while Warner is just meh. One reason for that is NiziU can actually travel to Japan easily as they are all Japanese citizens. (not sure of Nina though). So far none of the KPOP groups have been able to do that. Twice/BTS/Seventeen/Treasure etc.. just did video call promotions and did more or less the same level if promotions as well.