The reason for this, I presume, is because that the deceased person (bar case three, which is not exactly the same reason as the other two) continues to be the only man that did or was known for something, in your examples sentences. For example, in example number one,
If there has ever been a man who has been faced with challenges of opposition both at home and away, then it is King David. ...
The "something" is "faced with challenges of opposition both at home and away" here, and the person is King David. Since this sentence claims that the person (King David) is the only person in history (as is meant by "If there has ever been") that have been "faced with challenges of opposition both at home and away", it means that this event/statement still holds true to this day. This is exactly the correct usage of the present perfect tense[1][2]. Present perfect tense are used to describe "An action or situation that started in the past and continues in the present." This sentence perfectly matches this definition. The second example also have a similar construction:
If there has ever been a man who has been able to change the destiny of millions, it is none other than Prophet Muhammad (peace be upon him), the last prophet of Allah (God for some). ...
Thus, this sentence works the same way as in the first.
Finally, the last example:
... And if there has ever been anyone who has beenhas been president in the history of this nation who knew more about infrastructure.. than Trump I cannot imagine who it might be.
This one is a bit different. The person in question (President Trump) is certainly still alive, so this shouldn't fall into the "deceased people" example list. Also, the situation described is also (according to the source) still ongoing (i.e., Trump is still the president who knew about infrastructure more than any other presidents; this is a bit political though), thus the sentence is correct. In any case, all three sentences could and should use the present perfect tense.