There are so many fun and annoying cases, thanks for sharing yours!
A we consider a self-intersection because either 2 and 5 are exactly the same point or the segments 1,3 and 4,6 intersect very close to 2 and 5.
B we consider an intersection if and only if 2 and 5 are identical or 5 is "above" 2 (further up on the y axis). If 2 and 5 look really close but 2 is ever so slightly further "above" 5, it would not be an intersection even if it visually appears like one.
More details and a beta to try at Understanding invalid polygon (Self-Intersecting) issues in Collect - #15 by LN