Based on what the physicists have told me, the main issue with the Fortran code is that it is SLOW and hard to accelerate. Because the codebase is 30+ years old, much it sounds like it isn't well understood. They think it would benefit a lot from things like GPU acceleration, but that's hard to do with it in its current state.
Otherwise, the major issue is just that it makes a lot of assumptions and has a lot of inaccuracies, but that issue isn't due to Fortran but just because it doesn't capture all of the physics and there is a sim2real gap. So it DOES NOT have the right physics, but re-writing it probably wouldn't result in the "right" physics either.
The main version of the code they run uses 1-D physics (so one spatial dimension), which takes about 8 minutes to run on a modern CPU. The code can't be parallelized without being re-written. Running the 3D version of the code takes 1+ weeks for a single run, and that still has a big sim2real gap.