Just to chime in here and say that I have made a note of the issue with doubled-up notes when importing irregular bars; it still occurs in Dorico 4.
Also worth saying that the changes in Dorico 4 relevant to this thread:
also mean that pick-up bars are not currently handled in the same way when exporting MIDI from Dorico 4 as in Dorico 3.5, but we will remedy that as soon as we can.