"phasing" is a term I use kinda loosely...in relation to what I described, I'll try and explain more clearly!
Any distributor, for any conventional "distributor" ignition system, has distinct alignment points for all critical components.
The distributor "drive" must be properly aligned with the cam/crank drive, the point lobes on the breaker point cam must be properly indexed to the piston position through the cam/crank drive, the distributor rotor must be properly attached to the point cam so that it's tip aligns at a distinct point with the individual terminals inside the distributor cap. The distributor cap must be correctly indexed/aligned with the distributor body.
If the distributor is an electronic trigger model such as what you are dealing with, the same holds true, the reluctor/trigger wheel/whatever must properly align with the pickup module at a distinct point in order to "fire" the spark plug at the proper moment in time.
So "phasing" is a term I (and others in the ignition industry) use to describe the relationship of all the above "critical points"! If all components are original and unmolested, and/or the aftermarket parts are the correct version and design of the oem stuff, then all this "alignment" or phasing" stuff is a given...just install the fresh parts, make any necessary adjustments (like point gap or dwell or reluctor air gap, etc.), then verify base ignition timing and drive on!
But when performing modifications to this kinda stuff (like boneyardin' in distributor guts form one electronic distributor to a points distributor, or installing an aftermarket replacement trigger system), this phasing gets all outta whack, even just one or two degrees of "slop", misalignment, or plug cable terminals not positioned correctly is hugely magnified when the engine is running or even attempting to start.
In relation to your situation...the actual plug terminal (all of the eight terminals) in the prestolite cap, are "slightly" out of index (or phasing) as regards the engineered position that the reluctor/pickup provides to "trigger" the coil to fire the secondary side (spark plug). How much??? I don't know right now as I don't have the actual data or photographs I did about 10 years ago when I "analyzed" this particular issue!
At that point I also experienced the same thing you have found with your rig...common wisdom on the I-net at that point in time was those caps were interchangeable...if that was actually the case, then all aftermarket manufacturers would have certainly taken advantage of that detail...but...the "wisdom" was/is wrong!
I vastly prefer the male terminal distributor cap model (such as the prestolite or the delco hei)...I think it's superior in all areas to the female terminal system. But back in the day...those were certainly not in the mainstream of ignition design and most likely due to the proprietary nature of such as far as patents, manufacturing license, etc. They are also much easier to "treat" for the prevention of moisture/contaminants over the long haul, that keeps corrosion/oxidation of the terminal connections to a minimum.
So...guess it's time to run ta town and snake a prestolite cap, drill it full of "observation ports", and do an analysis again so we can prove or disprove this item. I've got tons of Holley caps (new and takeoffs), and points distributor delco caps (both sv and I-4 apps), but not a prestolite on the place right now!
This is a great topic you have brought up, this is the kinda stuff we hope stimulates thought around here and makes us put up or shut up! And we always back up our "ideas" with testing and report facts...whether the results are good or not so good!!!