It's sort of complicated because there's a lot of different events and options, and you'll only see some of those in a single playthrough based on your authority, civics, ethics, and RNG. If you want to know exactly what each choice does, you should look at the wiki page
here.
Behind the scenes, there's only four choices that matter. Three of these choices give 1 point to physical or virtual, while one of the choices counts for 2 points. These choices are:
1. What you did with your lost virtual pops in the synthetic fertility situation - putting them in synth bodies is physical, while leaving them in the building is virtual.
2. The digital refactoring event. This event happens first during the synthetization situation, and counts for 2 points. There are five versions of this event, one for each authority, and the options hint at which advanced authority you would get at the end.
3/4. During the situation, you'll get two random events about becoming synths, each of which gives you a choice worth 1 point. There are actually six different events that can happen here (two sets of three), but you'll only see two on any single playthrough.
At the end, whichever side has more points (out of 5) is given to you in an event. If you didn't have the synthetic fertility origin and your choices resulted in a tie, this event would give you one final choice between physical and virtual.
