On the new print organizer current active pltcfg file (set up with File->Print Setup) is the one 'chosen' to plot the print set, regardless of the pltcfg used to create the print set. I would think you might want to create a print set that included files using different pltcfg files? Shouldn't the plots be created with the pltcfg associated with the individual files in the print set and not the Plot Organizer -> Printer Setup pltcfg?Also, it looks like when I changed the Printer Setup for the pltcfg I really needed, I think it reset all my paper sizes to the default for that pltcfg which doesn't seem right to me. I have confirmed that. That would not be the preferred behavior.
No, multiple printers per print set is not feasible with the architecture of either Print Organizer or InterPlot Organizer.
There are many side effects that happen when selecting a printer driver configuration. Some are required, such as having to recompute the print scale and other layout parameters. Others are debatable, such as whether automation functionality in the .pltcfg such as the number of copies or the default paper size should be reapplied. The best approach is to first set the printer, then create the print definitions. The printer can be changed afterwards if needed, but the same side effects will occur in the print definitions that occurs in the single-Print dialog when a new .pltcfg is selected.