It is a contradiction, but it's also possible in a WS with a dead HoF that the orlesian Warden-Commander or some other warden goes in search of the cure and just isn't referenced. I'm a little disappointed that they wouldn't have included the Orlesian from DAA in the war table missions, but then again, neither Leliana or Morrigan knew that Warden more than a brief meeting or two, and it would have been a stretch for either to have claimed to have a way to contact her or him.
Yeah, trust me, no one is more salty than me about the Orlesian Warden-Commander not even being referenced in a tiny throwaway codex entry or something. The Warden-Commander was as real a character to me as my Cousland, and I care about her fate too. You're right in that Leliana or Morrigan have very little association with her (Morrigan a bit more, because of the events of Witch Hunt), but still... even a small mention somewhere would have satisfied.
Still, I'll admit in full disclosure that I also don't want the plot to go in the direction of a cure for the Calling, so I'm actually glad the issue isn't brough up with a dead HoF world state, because that counts against this subplot developing much further. I feel that curing the Taint cheapens much of what's unique about this universe in the themes of duty, responsibility, self-sacrifice, etc. If it's possible to defeat the Blight and suffer little to no consequence for it, then the whole threat of the Blight is empty, and the entire history of the Grey Wardens as the tragic champions of Thedas was all for nothing. There are no stakes to this fight anymore, if you can just defeat evil and cure yourself and walk away to a happy ending. I do understand that people may want happy endings for their Wardens, but this level of deus ex machina just feels... cheap.
Good summary. I'd add that he might have taken higher doses than normal while in Kirkwall under Meredith's influence? She was so fearful that she may have pushed people to higher doses so they were more powerful in case of trouble.
Good point, too. Samson's level of addiction was off the charts even considering he's older than Cullen, and Cullen's rapid degeneration could be linked to excessive use even beyond his time in the Inquisition. I don't think Meredith would have obligated everyone to intake more than the usual ratios, but she might have been less strict with than other Knight-Commanders, possibly encouraging those who took more than necessary because "the threat is everywhere" in her final more paranoid years, etc.
On the other hand, as we learn from Hawke (and Samson in Paper & Steel), the Kirkwall Templars pretty much just did whatever they wanted, Commander or not. If they could arrange a red lyrium farming and trade business right under Cullen's nose, they could be abusing the blue lyrium under Meredith's nose even without her knowledge too, so either way overuse back in Kirkwall is a good theory.