"He would have had to have been there" means that, in order for him to have accomplished whatever he accomplished, it would have been necessary for him both to be there and then to leave. In other words, whatever he was supposed to have done could not have been accomplished only by him being there.
Most commonly, however, the action done at the place is simply done at the place, and leaving the place is not required to perform the action. Therefore, we usually say something like, "For him to do what he did, he would have had to BE at that place," because merely being there is adequate to the task. Leaving the place has nothing to do with what he did while he was there.
A quick example: "For Watson to have murdered Lestrade, he would have had to be at Lestrade's apartment." This says it was necessary for Watson to be at Lestrade's apartment (given that the murder occurred in the apartment), but accomplishing the murder did not in some way require Watson BOTH to be there AND to leave.
Now, "have been there" is also logically quite possible. Let's say Sherlock determines that although Lestrade was murdered in Piccadilly Circus, the murderer couldn't have done it unless he had previously been at Lestrade's apartment to see Lestrade's calendar and thereby to know when Lestrade would be found at Piccadilly. In which case, for Watson to have murdered Lestrade, he would have had to have been at Lestrade's apartment beforehand; in other words, Watson would have had to be at Lestrade's apartment and also to leave the apartment (to go to Piccadilly to commit the murder).
Now, all this having been said, we don't usually construct the sentence as elaborately as in the first example ("would have had to have been"). It is not necessary to put the main verb into the conditional present perfect ("would have had"). We usually say simply, "would have to have been."
If you hear someone knocking at the door, you can say: That will be the milkman. This is a function of will that Swan (Practical English Usage, p600) describes as "expressing certainty or confidence about present or future situations".
The same applies to past situations. If you told your wife that you were in the shower earlier in the day when you heard someone at the door, she could reply:
That would have been the milkman.
In other words: I am pretty sure (or certain) that it was the milkman.
You could also retain the will in such a context: That will have been the milkman. And possibly even: That would be the milkman. But I see no conditionality in such a response.
Best Answer
This is an American regionalism that seems to be slowly spreading.
Here is a question/answer on it from Grammerly, which speculates that it will become widely accepted sometime in the not-too-distant future.
It's not terribly uncommon in the U.S., it's wrong in standard English, and it really annoys some people. The right way to say this would be had been, as you surmise:
But if you listen to Americans, you'll run into would have been fairly often, and if the speaker comes from a region where it's used, you might have a hard time convincing them that it's incorrect.