Oxygen to rootzones is a big factor, those little ramekin allow no air in, if you watered from top this also would compress soil further making it more difficult to germinate.
Try to allow water to absorb from.the bottom up into a slightly drier medium with alot more access to oxygen.
I dunno why people even bother with autos, imo having the clock ticking from day 1 is a detriment to new growers just picking up the trade. If those where photoperiodic there would be no problem whatsoever.