As far as the meters go, I dont have any idea about that. I’ve not seen that problem!
I would disconnect the yellow wires from the tube and measure them open. The only reason I can think of for the difference is that pin 8 has a load where pin 2 does not. Even at 5.5, that is a bit high.
It seems that your voltages are just high overall. I don’t know if thats due to a higher input voltage or if the PT you got just has some higher output. Really, around 330VAC on the red is what you are aiming for. 350VAC is high.