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They’re re-run, though. You don’t change the parameters in the middle of the simulation. That goes against the point of simulating something.
You don't rerun everything from scratch. Especially weather simulations can be checkpointed at places you have high certainty, and keep running forks after that point with different parameters. This is extremely common with for example trying to predict wind patterns during forest fires, you simulate multiple branches of possible developments in wind direction, humidity, temperature, etc. If the parameters you test don't cover every scenario that is plausible you might sometimes engineer it into the simulation just to see the worst case scenario, for example.
And in medicine, especially computational biochemistry you modify damn near everything
You’re confusing simulations of specific events with a simulation environment. If our universe is simulated, then it’s unlikely that the creators of the simulation would be interested in the individual occurrences you’re describing. The universe is what’s being studied, not the happenings inside of it.
Simulations of boats in water don't care about what's happening to the water much of the time yet it needs to be there, you seem to be way too confident in your conclusions
You’re still confusing a simulation of a specific event with a simulation of a universe. If you’re simulating a boat in the water, you need the water but you don’t need to build an entire ocean with fish and land near the water and buildings on the land. You just build what you need to simulate. We are clearly in a much larger simulation than one that would simulate an event.
If you don't know what they're testing that could certainly seem excessive. But failure of imagination doesn't prove it's impossible, although you can argue it's unlikely