The In-Betweener would find Superman Prime's opposite / negative elements sooner or later and cancel him out. The In-Betweener was able to force Mistress Death to destroy the original Elders of the Universe, even though these were actions against her will. She couldn't resist simply based on how his powers work in relation to the Marvel Universe.
It is even argued that the In-Betweener may be Galactus' actual counterpart, although that is up for debate. The In-Betweener is too deeply ingrained into the Universe' laws, that he would defeat GA Superman Prime in this case.
The opposite of the Anti-Monitors are the Monitors, so unless those two entities are merged, the In-Betweener takes this. Even if SuperMan Prime merged with either Monitor or Anti-Monitor, he still has not merged with his own counterpart, making him vulnerable to the In-Betweener's powers.
Now if one is going to argue that the Anti-Monitor is greater than Chaos & Order, that is another debate. You'd have to then argue whether or not a Marvel Universe is equal to or greater than a DC Universe based on their respective cosmologies.
I'd rather not have that debate here myself, but do as you will.
What I meant by no opposite was that Prime himself is from the Original DC positive Multiverse, who was then merged/infused with them energies of the Anti Monitor who is from the anti multiverse.
Thus Prime's opposite does not exist as I do not see the IB having multi multiversal power in order to create another SBP.
The Anti-Monitor's energies are from the Anti Monitor who is a megaversal power (multiple multiverses), the IB is sub universal. Just my take on it.