I do think you're right about the Doctor's personal storyline in the special being... like about his past relationships and not just one. We start out with a nod to Amy and Rory, for crying out loud! And then at the end, he says "Everything ends, and it's always sad," like a direct refuting of Ashildr's claim that there's beauty in endings and beauty in Clara's ending. I think this was definitely the Doctor feeling the weight of everyone he's ever loved, and it was bittersweet. (1/2)
(2/2) Also, you said you caught a reference to Sarah Jane? I must have missed that—what was it? And were there other nods to Clara that I overlooked? (Tbh I *was* really caught up in the cuteness of Grant and Lucy—and the Doctor in full Dork Mode. <3 )
The Doctor has faced a lot of loss and because of the kind of lack of focus in "Mysterio”, I don’t think you can peg his exact emotions and reactions to one specific relationship. And that was honestly what was impressing me for most of the runtime in the episode - however you chose to read it, you could kind of dig a nugget for your ship somewhere in there.
Because of this, I was thinking that the scene with 12 and Grant on the fire escape, where he salutes the universe for finding someone worse at romance than him, could be interpreted at things he let slip by. That really rang out to me as something like his relationship with Sarah Jane, which basically wasn’t allowed to go anywhere but there’s pretty clearly something there (and not just stuff implied from the New era).
In the big picture, I found this whole tone a hugely refreshing change from last year, which was just awkward and uncomfortable if you weren’t digging the relationship on display. I sat there like “wow, I actually don’t mind these implied romance cues because I am perfectly content with the ambiguity and thinking it’s Clara or something”.
Also Grant and Lucy were pretty cute so I was happy to have that to focus on.