Yet specifically on the Right we keep seeing how Netanyahu decides which parties should merge and which should run alone, and they generally play along.

I dont know if UTJ will split and each faction run separately (as Gafni is threatening) or if the factions will run together, as everyone else seems to want, but Netanyahu has already weighed in that they should run together. Who asked him? Let them run their own affairs. I get that he is worried Agudat Yisrael might not pass the threshold alone, but that is their business.

And now he is working on Smotritch and Ben Gvir. One day he wants them to run together and then another day the news reports Netanyahu is considering thinking of having them run separately because it might be better for him.

Personally I think the only reason from his perspective that it might be better for him to have Smotritch and Ben Gvir run separately is so that he can leave Ben Gvir out of the next government (if he should be tasked to form it), whereas if they run together it will be much more difficult, and there is no way Netanyahu wants Ben Gvir in his government. 

Either way, if these parties had any respect they would do what they think is best for them and tell Netanyahu to stop meddling in their affairs,.. As it is they just look like pawns of Netanyahu, there just to get him what he wants.