I never saw this “obvious” relationship, not to that degree. Yes, Kait did seem to be getting closer to JD, but as far as I could tell there was no girlfriend/boyfriend thing going on between them at that point. And well, the rest is history. Very much doubt there was anything going on after the fall of Settlement 2 at the very least. Doubtful there’ll be anything in that direction in the future between Kait and JD either.
Not that it will matter if TC decided the canon was JD not surviving the “choice”.
But yes, the voice lines are very unlikely to have any relation to whatever relations Kait may or may not have had in the past. Particularly when they trigger for killing Swarm. Or when they’re downed. For the most part, anyway, since there’s also active reloads and all that.