In the end I went back to separating the alternate Japanese platforms (ie Famicom, Mega Drive, etc) as much because I like to highlight the different platforms more than anything.
My process was to first import the platform that is the default in the LBDb (eg NES), and then create a new platform (eg Famicom) and import the roms using the LBDb default as the scrape resource, and with forcing dupes on. Worked for me.
Also I found that the scanning for new roms process will add all versions if there is no existing title, so an easy enough work around is to just delete the existing title(s) in LB and then rescan.