Hi and welcome to the forum! That indeed does seem a little conflicting. What you'll find is that ebikes with a rear derailleur need the pedals to be moving as you shift, just with lighter pressure on the pedals. This is probably why the Trek manual says to keep pedaling while you shift.
In your case the Bosch motors have shift detection anyway, which means that when you ease up on the pedals in anticipation of a shift, the motor will back off its power but still move the chain at an optimal speed when you shift.
So I would keep the pedals moving while changing, but just with very light pressure. Hope this helps!