It can become really complex. As an example, try to predict resonant frequencies on an entire plant full of rotating equipment. It can be done, but it often requires very expensive equipment and skilled technicians capable of using it to profile a plant. And that's just one potential problem you can run into.

We're often talking about custom plants here, or plants made in very low volume. Making a simulator for that can be prohibitively expensive, since you can't amortize the cost. For particularly important/expensive plants it still sometimes gets done. Though note the simulator might not be able to capture all the nuances of the real world deployment, so it might not be sufficient.

Meanwhile having a separate copy of the plant is also not often viable, once the plants get to any kind of size.

edit: After having 'someone' fact check and remind me: there are quite a number of simulation tools available that can sometimes partially do the work.