In most of large ISP networks, physical interfaces are used as switch ports (layer 2 port) and VLAN interfaces are used as layer 3.
Could you please explain what is the main purpose to use like this?
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Where does it use switch ports ? For transit routes ? for peering ? At route exchange points ? In general layer 2 ports are plug and play and do not need any explicit protocols to run. Hence preferred when the target is to lower overhead and CPU utilization caused due to various routing protocols and when unnecessary broadcass can be tolerated i.e in smaller networks. Secondly VLANs can provide isolation and basically split the LAN in different broadcast domain so can sometimes be as layer 3 instances. But these instances are logical and have obvious limitations.