Duplicate IPv6 addresses
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I do not know that switch... All I can tell you is that if your getting 2 address from two different RA then your not isolated at Layer 2 - its simple as that. Be it your switch config, or you have something else bridging the 2 L2 networks.
It makes no sense to me to run a vlan on top of the native interface if all your going to do is run 1 network on it.. Pointless... Now if your going to run more than 1 vlan on it, then there is something to be said to only tagging and no native.. But if all you have is native interface pfsense needs not now anything about vlans for that network.
But an "any" setting doesn't seem logical to me at all..
From you later image looks like you have every port as a member of 3 vlans - that is BORKED for freaking sure!!
I can tell you for freaking sure that is wrong without knowing that switch os at all...
The only ports that should be members of more than 1 vlan are ports connected to something that will sep the vlans based upon tag, etc.. Like a router interface that has more than 1 vlan on it, or a another switch uplink, or connection to an AP, etc.