I think the freshly cut end reason ... is just because sometimes the end becomes a little frayed. That too, might be something that might vary from one brand/weight/type of thread to the other.
And too, sometimes when working with the freshly cut end, and I've had problems threading it, it will have frayed and need a new cut to get it threaded.
That being said ... lots of times I have threaded successfully from the old cut.
Honestly, I never think of which end I thread ..........
In the end, I don;t think it really matters what end you thread ... just do it, and enjoy the project you are working on!