SpaceX built an incredible custom simulator in order to design the methane engines used in Starship[1]. Right now they are experimenting with manufacturing techniques, which is much less amenable to simulation
Elon has stressed this. Design is easy, building is hard, building at scale is harder. Thus the reason he iterates on the design is to make each design iteration also an iteration in the manufacturability, not just the functional design.
[1] https://www.reddit.com/r/spacex/comments/2zhad6/spacex_at_gp...