It is correct that you cannot do so through the console.
if someone could tell me what command to use and how to input it. Is there a way to change their de jure? I suspect the only option may involve a complicated debug command, and while I'd prefer another option I'm 100% willing to use debug to accomplish this. I've considered just handing them out with the duchies when making the custom kingdom, but I don't think that will actually alter their de jure. As far as I know, you can't de jure drift counties into new duchies. The loose counties are a different matter altogether. The duchies aren't a huge problem, I'm not playing Ironman and I have debug enabled, it wouldn't be that difficult to give all those duchy titles to one guy, give him independence, switch over, make a custom kingdom, swear fealty, and switch back then de jure drift the new kingdom in.
It's wonderful and amazing and I love it, but there's one problem: I have all these loose duchies and counties that aren't de jure part of it. In my current game I've made a custom empire containing every island on the map.