I would agree with your statement, I also cannot believe people are still using that wretched native vlan as it confuses the hell out of most people, it breaks more than it fixes /rant off.
that statement above is preventing VLAN 4 to go across the trunk, because you are not allowing it. even though you are forcing vlan 4 not to be tagged by defining it the native vlan, it is still not allowed.
if you were to make it switchport trunk allowed vlan 4-6 , on both ends of the trunk, it should work.
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