Simulations are physical systems just as much as running a "Hello World" program on your computer is a physical system: somewhere some transistors flip, but they are not relevant for the level of description we are interested when running the program, the program output, as simple or complex as it could be. Somewhere in the brain some molecules do "stuff", as a result of the "stuff" the brain sustains one agent, or more [1]. How exactly, in an engineering sense, the agent is constructed is yet to be discovered, hopefully we are only a few years, a few decades, away from building synthetic agents.

Sure, we have about 2,700 years of tradition speaking of souls (considering the major religions: Christianity, Islam, Buddhism, Hinduism, and Judaism). Where did those 2,700 years got us? Has any religion been able to build a conscious agent starting from basic materials (whatever they consider basic, pixie dust if they will)? Have all this years speaking of souls managed to achieve something meaningful, even as a side effect, that actually improves the quality of life? I'm talking hay [2], indoor plumbing, hook-and-loop fasteners, ibuprofen, GPS, voltmeters, extreme ultraviolet lithography, things that you and I can use and rely on daily. I have read pretty much all the major texts of the major traditions, from Mahābhārata to Summa Theologiae, call it intellectual curiosity. If not for the "bragging rights" to say that I know what filioque or bodhipakkhiyādhammā means, I would regret it, wasted time and pointless eye strain. So no, it's not nonsensical and unscientific to rule out a not even hypothesis such as the "soul" after 2,700+ years without any kind of results and absolute incompatibility with the way we actually interact with the world, scientifically or not: photons, atoms, electromagnetic fields and the like.

[1] https://en.wikipedia.org/wiki/Dissociative_identity_disorder

[2] "The technologies which have had the most profound effects on human life are usually simple. A good example of a simple technology with profound historical consequences is hay.", https://quotepark.com/quotes/1924489-freeman-dyson-like-many...