I could well be imagining it, but here goes.
One of the elements of this series, as we've discussed, is how distant the Doctor has seemed. Some of this has to do with the decisions he's taken and how point of view on those and I don't want to dissertation on that all again with the swearing, but the distancing has partly been to do with how the Doctor has worked within scenes and episodes.
Looking back and I can't completely verify this without watching all of it again, but looking back I don't remember many scenes in which the Doctor has narrative agency, in which the scene is about him and his actions, without it being seen through the eyes of another character.
Agency within a scene is often kept pretty invisible unless your attention is being drawn to it and created through a mix of camera angles, close-ups and reverse shots designed to draw your attention to who's reaction in a scene is most important.
A classic example from Star Wars, because everyone uses Star Wars, is in the Death Star scenes at the end of Jedi, which are all about Luke's reaction to the Emperor. Throughout we keep cutting back to his face, in close-up to his reaction of the ensuring murder.
Or most of Citizen Kane.
In Doctor Who terms, when the Doctor and Clara are in a scene together, the narrative agency is all with her. It's been like watching Rose's reaction to the Doctor in Rose for eight episodes.
In pretty much every scene we've been seeing the Doctor through the reactions of Clara and in key moments when we might previously have followed the Doctor somewhere, for example into the crust of the Moon in Kill The Moon, previously we might reasonably have expected to follow him and make the discovery with him.
About the only episode in which this "rule" is properly broken is The Caretaker notably in the moment when he reacts to Clara and the man he thinks is her boyfriend as they walk away.
The Doctor when he's alone indeed has had a fair bit of agency. Right through Flatline in fact. But whenever Clara's been part of the conversation, it's still about her reacting to him.
But there are, and again, I'm willing to accept if I've missed one, but there are no scenes in this series in which we see Clara through the Doctor's eyes.
Except, in Flatline, right at the end, we suddenly do.
It's at an interesting moment too - just after he gives his "I am the Doctor" speech.
In the next scene when he's dropping everyone off and Clara says her goodbyes, whereas previously such things have happened with the Doctor almost skulking in the background suddenly we're getting close-ups, reaction shots from him watching Clara, questioning Clara, who's standing in a mastershot or mid-shot much smaller in the frame.
I don't want to fill your screen with these little screenshots, so go back and watch the ending and I think you'll see it too. Suddenly Clara's back to being the one the Doctor's curious about as per last series and in every shot she's in the Doctor is a presence, over the shoulder, in large close-up or completely within the frame.
That's why Clara, who's been our hero for the past forty minutes suddenly becomes a mysterious, slightly sinister figure again.
At the very end of this scene when the Doctor's entering the TARDIS it seems like we're back with her. He's walked inside and there's a big old close-up as she considers what he's said about "good not having anything to do with it" her eyes giving every indication that she doesn't understand.
Except within seconds we realise that the agency has in fact passed invisibly to Missy watching that reaction on her iPad. Which means timing wise, Clara stops being the main figure in the episode from the moment the energy reinvigorates the TARDIS and seemingly the Doctor within.
Peter Capaldi, now, is the Doctor, just as he says he is.
One other note: the Twelfth Doctor mourns the deaths, properly mourns them. Ok, yes, he says the wrong people may have died, but that's not unusual. He goes there in Voyage of the Damned, but in a switch it's him lecturing Clara about morality and mortality.
Now, it's possible he's testing her, trying to work out why she's not mourning them too. Why she's being so cocky. But I don't think so. I think he's genuinely being compassionate for once.
It's almost as though when he said, "I am the Doctor" this incarnation finally believes it and his wrestingly back of agency from Clara, the music and his more obvious sentiment in relation to the loss of human life could signify that. Effectively it's taken nine episodes to get to post-regenerative point the Tenth and Eleventh Doctors did in an hour.
Goodness knows what any of this means. Could mean nothing. Could be in the next episode we're back to the status quo of the previous eight episodes, me loathing the Twelfth Doctor, Clara in charge, all that business.
But, and it's a small but, it's also possible, that the Doctor's agency will continue, or we'll be back to the joint Time Lord / companion agency of previous series and that we could reassess his behaviour this series as post-regenerative torpor, about him learning to be the Doctor again. If that is indeed the case, I wish they'd made it clearer...