The Ford separators I've seen drain the oil back into the crankcase and contain a mesh - like medium that acts as a course filter. A small amount of water shouldn't be an issue and will easily vaporize in hot oil.
Considering this is a direct - injected engine, I would much rather have it drain back than to enter the intake where it could never be cleaned from the intake valves. Those are the only two options unless you install a catch can.
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