Hi Glen,
Perhaps I'm stating the obvious or something that's out of scope for what
you have in mind.
However, one property where they differ is that a physical link has a
physical capacity for carrying traffic (i.e., bandwidth).
A virtual interface inherits it's capacity from the physical link(s)
There are certain protocols and mechanisms tied to a physical medium or MAC
layer. If you are doing L3 tunneling you lose those options, if you are doing
L2 tunneling you may lose less of them depending how transparent the tunnel is.
Things like Ethernet pause frames or 802.3ah instead of BFD
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