I’m not sure if this solves the problems you are having but have you tried the append feature in PCBNew? If you open it manually, not within KiCAD’s application launcher, you have a new menu options for appending things to your PCB.
So, if you start with two separate KiCAD projects with the end product being two different PCB designs, you can then close everything, open PCBNew manually and bring both PCB designs into a third PCB design using the append menu command - its just like you’d imagine panelization working. I did this to nest two boards together with dead space in one that would have wasted money.
Here’s a link to the results of what I did. Hope I didn’t completely miss the boat here on what you were trying to do.