It was a shrine
You watch an episode dozens of times, but it’s a chance comment from somebody that makes you look at it entirely differently. I was watching one of those YouTube reaction videos for “Heaven Sent” and the guy pointed out that the flowers in the portrait room were lilies. I’m not much of a flower person so I honestly never recognized them as such.
And then I realized: This wasn’t just a bedroom where he randomly placed the painting of Clara that he (according to Moffat) painted.
This was a full-out shrine. Her portrait in a prominent place, where the sun can shine on it. Candles nearby. A somewhat sombre atmosphere to begin with. The Doctor later coming back here to be with her portrait.
This was Clara’s shrine. I’ve known people who have set up similar rooms for lost loved ones. Often it’s where their ashes are kept, too. The fact there’s a fireplace here, a place where you’ll usually find ashes, couldn’t possibly have been intentional symbolism … could it?