In answer to your point, there are a number of heat related effects that could reduce the spark. As the coil warms up, its resistance increases reducing the primary current, the electronics in the control unit will be heat sensitive which could impact the spark, breakdown voltage of the cap and rotor arm will decrease with temperature and could also impact the spark.
If the rotor arm was in the wrong place when the points open, this would increase the gap the spark needs to jump, and could make an otherwise healthy spark marginal, so that any heat effects would be more likely to effect the running of the engine. All hypothetical of course, but it does seem to fit the OP's symptoms.
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