Is that not in there? If you go and get Morrigan and then begin the plot with the Grey Wardens, there is a period where Alistair or Loghain is potentially at Skyhold at the same time as her -- and there is a scene between the two of them if you go and speak to Morrigan. Might only be if they were involved in the Dark Ritual, I don't actually recall, but I don't think so.
The triggers must be broken. I definitely did not have any interaction between Alistair (as Warden, romancing a mage HoF, with OGB) at any time between Morrigan's arrival and the Choice in the Fade. And I put that off for as long as I could. He didn't mention Morrigan at all.
The mod group have found the conversation. It simply will not trigger. The current theory is that it was cut, though, not broken.
[ETA: now I've read the thread, I see, bugged, or way-too-specific, not cut. If the only way to get it to trigger is to do Halamshiral first, then get the Warden... well, bummer--because logical story progression--the way the NPCs talk to you, Leliana talking about getting the Warden, and the first storyline Skyhold quest being "Talk to Varric on battlements" etc--would have a majority of players pick up Hawke/Crestwood (and therefore Alistair/Loghain) first. So, it seems it just won't fire for most.
So, my theory is now that the triggers only allow for "Morrigan present in Skyhold" before Alistair/Loghain arrives.
Seems like a less specific trigger might need adding?
*trying to decide if I should nix 50 hours of play or just restart game.....*]
Side note: Fiona in the same Keep, and he talks about the HoF needing information from her. No option to say "hey, she's here!" *plot hole brain explosion Grr*