Using a "native VLAN" on a trunk means not tagging this VLAN. This is not needed for Extreme EOS nor ExtremeXOS. I would recommend to tag every VLAN on any inter-switch-link. Note that some special configurations (e.g. RSTP on EXOS) do require a native VLAN, but those situations can usually be avoided (e.g. using MSTP instead of RSTP).