I believe you are right victor.
I found myself in the past counting for crank pulses after TDC mark, to be more sure about timing events and angle, not trusting the rulers.
The picoscope software rulers are a good tool, but we need to remember that the angle shown has the assumption that the engine is rotating at constant speed, so that the angle could be guessed as a linear relation to time.
In an engine with one or more disabled cylinders, and all type of problems we may find, we could have a very unstable speed in the engine during the 720º.
If the software could use the crank sensor, as you said, especially with high resolution ones (60 tooth or more), we could have a better angle guessing than just using time relation.
Small feature request!?