I would surmise that Tomorrow and Tomorrow and Tomorrow has somewhat altered the main timeline, and there could be some minor adjustments with the characters to accommodate the story that showrunners want to tell.
I'd consider the Pike/Kirk relationship to be a minor thing. If they meet again, I'd be okay with it if the story broke some of the canon. I mean, they already changed the timeline of the Eugenics War, so is it a huge deal if Pike and Kirk come face to face a couple more times throughout the series?