I would drop the chain , turn the cranks to see if there is any grinding or noise coming from the motor.
If it is from the motor it should not change as you put miles on the chain. If it is from the chain and once you put miles it goes away then probably some cogs are worn out, I am not aware of any breaking in period for chains, they just match the cogs if they are worn out.
Moreover Bosch gen 2 has a reduction gear and these gears can be felt slightly when pedaling.
Other than that that grinding feel may come from anywhere on your drivetrain. Derailleur, even from worn out pedal bearings.