I have a powertap hub and powertap P1 on my bike and I notice the same thing. My difference can be anywhere between 2-10% based on how clean/lubed my chain is. I’ve actually seen it start around 2% and by the end of a 10hr ride be closer to 10%. I’ve been riding with this setup for 3yrs. I do not believe it is an issue with either power meter. IMO both are working accurately and consistently. It’s just a difference in where it is measuring the power at.
I would chose 1 power meter to follow and not worry about it. I would use the pedals, since drivetrain losses can vary. The measurement at the pedal really is the best as it has less things that can effect it.