ad 1) Earlier in this thread someone had the experience it was impossible to add a free visa after booking.
ad 2) Seems questionable. The free transit scheme is clearly linked to a stop in SA with a SA carrier. I would assume the visa is gone after cancelling the flight, or that the visa is linked to a specific PNR and flight number. If not, this would be a loophole that gives free visa away that they certainly will close. If you book fully refundable no further harm.
Re others: no clue....

And mnlfqtv : you apparently can plug in one stop in a return flight - I highly doubt you can leave the Kingdom during such a stop, again seems playing with fire. If you can't, at best you lose your DXB ticket if they do not let you board, but at worst you find yourself in DXB without any option to fly back to JED and catching your flight there (or even worse - JED airside without an option to go to departures or leave the airport). Note that in the majority of cases regular visa for countries are single entry and multiple entries have to be asked for specifically. But maybe you can simply call SV what the rules are....