I followed your path, sold or scrapped all that Motoplat stuff *, because of bad cable insulation, weak sparking, failing coil units, and non-servicability due to extensive encapsulating. Ducati Energia parts showed up much more reliable over the years. My own 350Mk3D ran more than 30000 km with a Ducati CDI and a DIY-converted 12Volt Regulator/rectifier.
My period of maximum activity with (mostly w/c) Ducatis was between 1985 and 1999, approximately, when a lot of abandoned singles - mostly SCRs - were imported from Italy to Germany. Hence, my experiences with Motoplat alternators are a long time ago, so details are somehow obfuscated.
I agree with your explanation of the important facts - parts certainly may be mixed if radial clearance (i. e. air gap) and length/width of pole pieces and magnets are roughly matching. And indeed, the shape of the voltage pulses is of no importance for the charge rate, or average DC voltage at the battery terminals.
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* I also discarded all the Ducati brass flywheels, as their tapered seat often loosened in operation, then damaging the crankshaft taper, despite having appling the correct torque on the fixing nut. All my engines were equipped with aluminum rotors.