I’ve been thinking about this problem just now, and have a couple of suggestions/questions:
Would it be possible to construct a printhead (standalone or for the flux), similar to old inkjets, that sputters microencapsulated metals that are suspended in a colloidal solution onto a substrate – the solution made to evaporate after printing? The metals left over would then be exposed to heat (maybe microwaves or laser) and flow together to form fully metallic traces with resistance typical of a conventional PCB. Thickness of traces could also be varied very precisely using this type of printer, and resolution would be extremely high.
A second pass with a different head could print insulation material and/or 3d structures. Using an insulator that is thermally conductive would allow the direct printing of (3d) heatsinks on the PCB. Perhaps the substrate itself could be first printed using the insulator material, leaving holes where needed so no drilling is required, meaning that from start to finish the printer can print the entire board.