Thank you. I think you told me enough to understand how to best think of and use the data in this respect.
I'm playing with the idea that 3D "molecular plot" is intended to be a 3D representation of "Nomenclature of Organic Chemistry" (CRC) (so that non-planar molecules can be seen easier than they can be in the associated 2D chart). I'm unsure of this. (but this section contains many rules and abbreviations of chart that have nothing to do with bond angle or 3D structure: abbreviations useful for those saving paper as well as some that are for bond abbreviatons)
But According to new iupac pdf on graphical representation: what kind of bond isn't always specified but should be consistent - which i consider awful. (but that short document mentions salts are "non-structural" and ions are best kept separate rather than connected in the 2D graph).
I see "Everything has it's place", in this "historic 2D annotation model", is not true.
Thanks you answered my question. I see now Mathematica is doing "what is generally expected". It'll be much easier to navigate around knowing that.