Here is an example using REW (Room EQ Wizard), compared to a recent measurement.
The simulation isn't too bad down to 70 Hz. Below that point it becomes useless. It doesn't account for the bottom end gain which extends the subs down to 15 Hz even when their nearfield plot is rolls off around 25 Hz. The massive 45 Hz mode was not predicted at all and I've found it to be the most audible issue. If it isn't pulled back the subs boom.
Red: measured response
Green: simulated waterfall
The irony of room mode simulation is that you actually need a real measurement of the space to be able to tweak the simulation and get it reasonably close. Otherwise, it's difficult to know where you can trust the model and where you can't. With a bit more time I might be able to figure out what is going on, but if you are using the simulation to show which of different room designs are better, will it really help? At this point it's difficult to say.