@user_3445655 hello,
first of all, the layer 3 VNI is a very important thing.
you might ignore the affect of the VNI during the routing information spreading. But when the packets forwarding, it will be encapsulated by the vxlan, the remote peer VNI will be contained so that it could be forwarded to the correct vpn instance based on the encapsulated VNI. After that, the packet are forwarded in the vpn instance.
for the second question, when the packets arrived, if the VNI matches the BD domain VNI, it will be transferred to the BD domain(this is a layer 2 forwarding). If it matches the layer 3 VNI, it will be transferred into the vpn instance. So, if the VNI is same with the BD domain VNI, the router cannot distiguish them from each other.