Most O.E. ignitions were actually just holdovers from the old 6 volt days. When they went to 12 volt systems, they just stayed with the 6 volt components and reduced the system voltage accordingly. A typical budget committeel compromise it sounds like.
Since they can actually handle 9 volts pretty well (more heat was the big problem I think), and the condensers could live with that for awhile, they stuck with that value I guess. Probably figured that any more resistance in the primary wire (to bring it farther down towards the 6 volt region) would build up too much heat in the wire. And it would also reduce spark intensity to the point where the them new-fangled engines with high-compression and all that wouldn't run right. So they stuck with 9 volts.
Until FINALLY they threw some money at the problem and built systems that would run on the full system voltage and give more spark. Of course it was probably emissions regulations that finally made them step up, but that's just a guess.
Lots of replacement coils can handle the 12 volts by either using internal resistance or just designing them to handle the added heat. Most aftermarket ignition modules run on 12 volts too, so you can have your cake and eat it too.
Watch out for the cheapie replacements for a Duraspark though. Some of them don't like 12 volts even though many of the Ford ones ran on full voltage originally. This might not be a problem any more as I would hope that most aftermarket manufacturers have figured out all the subtle differences between all the different Duraspark models and don't scrimp where they can't get away with it.
I went through 3 Kragen-bought modules ($19.95 specials) before buying the Ford Racing (MSD built and $100 some-odd bucks - yikes!), and then an MSD Adjustable-Timing-Control (even more!), Duraspark boxes and it's been happy ever since.
More spark... Goooooooodddd.
Paul