I think the only time they've ever planned ahead like that was with Deadly Alliance, and setting up the idea of the Dragon King for the following sequel. I don't even think they planned for Blaze to become what he did in Armageddon. And Shinnok's appearance in MK11, but that's a bit different, since it was a bit like history repeating itself. And even with MK11, they did kind of set up the idea of Dark Raiden against Emperor Liu Kang as being the next major conflict in the series. With Kronika and the future past storyline, it seems like they later decided to make that conflict a secondary one, if significant at all. So yeah, I very, very much doubt they were planning for Kronika, or even this general direction in the plot.

Based on various interviews and things I've heard, as far as I can tell, when the time comes to start pre-production of the next MK, that's when they get together and conceptualize what the game will be about, story wise. And yes, I'm sure they often look to previous games and consider what little random characters, mysteries, or visual nuggets they can expand on to make it seem like those things were foreshadowing. But even then, I never got the impression that they were trying to put on a pretense like all those things in the previous games were something they were planning from the start.