Horses, not zebras...
Fender doesn't have a guy sit down and wind a transformer as he builds a Champ. It is REAL unlikely they made a run of transformers with the wrong size wire. But anything is possible.
Looking at a 5E1 for example, note the B+ goes to the screen, and then through the OT primary to the plate, so it will always sit there with higher screen voltage. Then compare the 5F1 where the B+ comes off two nodes, and the screen is 10k downstream from the plate, so it will be different there.
If we assume a 1k screen node resistor, and maybe 5ma current through it, that will drop 5v from the B+ supply, but the 6V6 draws a lot more plate current than 5ma, and through that 450 ohms it drops more than 5v, and so will have a lower voltage.