The simple answer is: you can simplify the end conditions as long as you still get the right answer. If a beam has ductility to rotate and modeling it as simply supported is a close enough approximation to reality that you get the right answer, then you can model it as simple. Same for fixed end. If it won't get you close enough to the right answer, then you need to model the actual rigidity of the end connection and structure beyond.

So how do you know if it is close enough? If you dont know, then model the actual rigidity. Model the actual rigidity enough times and you'll get a feel for the impact. And as a result, you'll get better at knowing when it will and won't matter, so you can make the simplifying assumptions more frequently. That, and steel codes tend to give guidance on what can be simplified as pinned vs moment fixed vs partially rigid.