Come to think of it, I think the "Port Emulation" feature on the Every and WiFi2 "fakes" the PORTB/PORTC/PORTD of the original Nano/Uno, rather than just providing familiar names for the new ports. So "PORTD = 0x12;" will end up as some combination of writes to bits of the 4809 ports A, B, C, and F, while "PORTE" remains an new-style structure (defined NATIVELY, not by the compatibility feature) for accessing the 4809 PORTE features.
To access the 4809 ports in native mode, you'll need to turn OFF the "register emulation" in the TOOLS menu. And you'll find your port bits scattered all over 