While I still think my first idea is better for a number of reasons, I thought of another way this hypothetical sequel could work and still tie into the main timeline.
We know of at least one canon timeline that exists where the events of CT took place, which would be the Radical Dreamers timeline. It is possible that another, if not the RD timeline itself, did not have Dalton raise an army in Porre and attack Guardia. Here the Kingdom would have flourished and Crono and Marle would have become the King and Queen. However one day a Dimensional Distortion, potentially as a long term side effect of the Time Crash, causes Crono or someone else from the original cast to accidentally travel between timelines into the one that the Fall of Guardia and Chrono Cross takes place. Once a way to travel back and forth between timelines has been established (Marle does have the same amulet as Schala afterall), they would not be able to turn a blind eye to the fate of their Kingdom despite it not being from their own timeline (similar to how Crono and gang could not ignore the day of Lavos, long after they would have died). Then the whole resistance scenario I mentioned before would continue from there.
However like I said, I still prefer my first idea overall for two reasons. One is because this would employ Dimensional Travel and Time Travel together, which could get very confusing if not done properly. The second is that it might feel too samey to how Serge gets pulled into a timeline where he had died. The only real difference is that it would be Crono and the fate of his kingdom vs Serge and the fate of Schala. One thing I find funny is that Square made sure to leave that record from Radical Dreamers in Chronopolis to establish that it was indeed canon, despite Kato himself feeling it was incomplete and just a Chrono Cross prototype. Could it be possible that something like this could have already been hinted at in reference to Chrono Break before the project got canned?
That record was the real difference maker, because even though Dinopolis itself had already confirmed multiple realities aside from the split that took place in Cross, but it also confirmed that the events of Chrono Trigger happen in more than one primary timeline as well.