It's not the lecithin/choline that's the problem. It's the particular bugs in the gut that break it down that are. The correlation is between disease and blood concentration of TMAO(trimethylamineoxide), which is a breakdown product resulting from bug metabolism.
The inconsistent results of studies showing the effects of lecithin on cholesterol and HDL may be do to the lack of control of gut bugs in the lecithin effect studies.
I'm reading this as saying it is the amount of choline determining what the gut bugs do with it.