They are wired series instead of parallel, because that is the way it should be done.
One coil is firing the cylinder under compression, the other coil is firing into the exhaust stroke(waste spark). If you parallel them, then the coil that is firing the waste spark fires first, and will reduce the energy going to the coil that you want to fire. When they are in series, both coil primaries see the same current.
It only matters which coil you use, if you want it to work. If you keep the stock ignition, you need to match the inductance/resistance of the sum of the 2 coils(since they are in series) to approximately the values of the stock coil. This will ensure that your dwell settings in the ECU will properly charge the coil at higher RPM, and not cook the coil at idle.
IF you convert to CDI when you do a COP, it reduces the coil matching issues, because a CDI doesn't need dwell. A low resistance coil is better, to keep the CDI from overheating the coil. If you don't convert to CDI, then your COP will likely not perform as well as a good condition set of stock coils.
Not familiar with which Ford coils you are referring to, but on some systems it trigger the coil to multispark from the OEM ECU. The coil itself may not multispark without the ECU telling it to.