Yes, I'm finding the same thing when positioning my Jaegers in front of my line infantry; my guys definitely do still take friendly fire from the line infantry. This occurs even if I am fighting against an all-melee opponent, so it is definitely FF.
I suspect what people are observing as the skirmishers being safe from friendly fire by ducking is actually the fact that most of the line infantry shots would go over their heads anyway even if standing or through the gaps in the formation.
The only way I've found to get two rows of units one in front of the other firing without friendly fire is favourable terrain (which, incidentally, is a very handy method of effectively doubling the firepower of that section of your line).
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