Transfomr init code called just after duplication (presumably before regular depsgraph update is executed) would erase new objects' transflags. This is more like a hack than a real fix, but since that transform piece of code is already a hack... Other solution would have been to force DEG to run after object duplication, think it's better to go with that solution for now. Not to mention to fact that dupli flags are put into transflag... ;)