Ok, let's look at your sentence:
"-Whoever did that must be a very brave person.
-Only a very brave person could have done that?"
In your example, whoever is speaking is not absolutely certain of what he's saying.
He's pretty sure that a brave person did something, but he's not stating a fact either. You can figure that out by looking at the modal verb must in your first sentence.
In other words, this situation is hypothetical, thus the use of "could"