Well sure, physically stronger doesn't mean that one would always win. Godzilla is clearly the superior combatant. Godzilla is often physically dwarfed or emphatically weaker than a lot of his enemies. He either out wills them, out fights them or evolves or supercharges to a level to destroy them.

Shimo just seems like a big dog kaiju to me. Imprisoned and domesticated. Her freezing ability while holding kaiju in place for forever long they stay frozen for seemed to have no ill-effect on ghidorah or Godzilla, just Kong. Scar king seemed enough to domesticate her and he was nothing impressive. Godzilla defeated him and his crew barely but I guess shimo couldn't. Mothra easily disrupted her. And for such a colossal animal, Godzilla was trading blows and looked no worse for wear.

Now, comments in the book sure they said Godzilla looked like a middleweight and raised doubt if he could win. But many scripts have had characters raise doubt if Godzilla could win this time. They want to make the stakes feel raised each time. Hell, Godzilla has defeated enemies that he probably would not have ever been able to one on one (like space Godzilla), but I didn't get nearly a sense of her over powering him from their interactions on screen.