I took Terrifying Presence on my first character, as I like to have all the dialog perks (even though they tend to be redundant with having a high Speech skill anyway in many cases). I was a little surprised at how infrequently it came up, so I figured maybe I took it too late to see every instance of it. Checking the http://fallout.wikia.com/wiki/Terrifying_Presence on the perk, though, I only see the instances listed that I saw myself...

Grecks can be frightened after taking his money for the Debt Collector quest.
Jean-Baptiste can be convinced to give Cass a little more time to live.
The Brotherhood of Steel troops that track Veronica down at the Follower's of the Apocalypse Outpost can be frightened into temporary submission.
Benny can be scared before you brutally murder him.
You can tell Ceasar you want to paint his tent with his guts.

Can anybody recall another time it comes up? Not sure if the wiki is up to date. If this is it, I kind of recommend you only take it if it's central to your roleplaying experience. As it was, I couldn't even use it every time, as I was playing a "terrifying" good guy. It's not like I was going to use it just to be mean to Grecks or Benny. In contrast, I kind of appreciate dialog perks that give some other constant (even if small) bonus, like 10% damage against a given gender. At least then you don't feel like "this will only ever come up three to five times in the entire game."

Its not a very useful perk for a "good" character and as you said, its kind of redundant with high speech.

I believe that you can use it at Helios 1 to scare off the NCR.

Otherwise, you can use it on NCR or Legion hit squads that try to intimidate you, making them flee in panic.

I used it on 1 play through and those and the ones you listed are the only times I remember it being an option. (Jacobstown NCR mercs too. . .maybe? I can't recall)

Its basically just the same as the "attack" speech option with slightly more eloquent dialogue - well that and it makes your opponent flee instead of get violent.