Q. If I connect virtual networks together via ExpressRoute are they connected using the Microsoft backbone?
A. When using ExpressRoute there are really two connections in play, the link from the organization to the peering provider and the link from the peering provider to the Microsoft datacenters. When connecting virtual networks together via ExpressRoute all of the traffic between virtual networks will flow via the peering location, i.e. it will leave the Microsoft network, go to the peering location and then back to the Microsoft network. This applies even if the two virtual networks are in the same Azure region. This means potentially there may be a higher latency than if you connected the virtual networks together directly using vnet peering (if in the same region) or with site-to-site VPN (although this has lower maximum speed even with the high-performance gateway).