Just because the seeds planted in stories like Shattered Empire didn't manifest in TFA and TLJ doesn't mean they weren't always meant to connect to Episode 9 all along. There's no compelling reason for the big reveals in TROS to have been spoiled by TFA or TLJ. The first two movies just needed to establish the key players, establish a central conflict, and make money. They did that. Having a more specific OT-related backstory to the conflict we've been watching is something that, frankly, works better if it's saved for the end.
I think RJ got more freedom than most would, but I think he was working under the general parameters that LFL had in mind for where this ST story was going. By all accounts, he worked very closely with KK and the LFL story group, but was being allowed to shape certain elements that wouldn't interfere with the key aspects of how Episode IX would end. I don't think he was going rogue with TLJ, or with where the end of the saga was meant to go; KK isn't shy about firing writers/directors if he were.
If I'm not mistaken, Colin Trevorrow started writing his version of Ep9 *after* RJ had finished writing TLJ. So it has always been a linear process, and LFL has been guiding things in both the movies and the other materials to connect with one main vision for the ST story. In fact, it was because Trevorrow wasn't seeing eye to eye with LFL's vision for how to end the saga that he had to be replaced.
I know you will disagree with this, but RJ knows what he's doing. He trimmed some of JJ's "mystery box" concepts that would have potentially made for a convoluted mess, and cleared the way for a more streamlined and focused final chapter. He did what needed to be done from a storytelling point of view. And I would have to believe that he did it while not breaking from the broader LFL outline for the ST. To believe otherwise is just tinfoil hat stuff, imo.
Very glad to. I think the Palpatine Contingency references being in the TLJ novelization backs up the notion that there's been a consistent (if perhaps vague) general plan in place for what we'll see unfold in December.