On youtube there's a guy named Kinetic cycle coaching. One of his videos (I think on saddle setback) said he measures 12cm from the back of the saddle, as that's roughly where people sit. And obviously since it's from the back, it is not bothered by short-nosed saddles.
On my saddles, I put a little grey mark underneath on the saddle shell, at that 12cm from the back point. Then when measuring saddle height, I am measuring vertical from that point (i.e, to the surface above that point).
I won't say the 12cm is perfect between various brands and designs of saddles, in terms of where a person would sit. So marking 12cm, or anywhere really, if nothing else, is a good way to be able to reproduce the preferred saddle height using that saddle, regardless if you move the setback around.
Having spent way too much time figuring out what the saddle height should be, where I seem to be comfortable is to get into the saddle, clip in, pedal for a bit to where I'm sitting comfortably in the saddle. Then staying there, unclip and do the heel on pedal, which I choose to do on my left side as I know my left leg doesn't extend down quite as far.. so I set the SH based on that. I find that if the heel of my cycling shoe just grazes the pedal surface (using look keo pedals) then it's about right.