In the context of RFC 6177, "IPv6 Address Assignment to End Sites", an end site would be a single location with its own dedicated IP service provision.
That definition might encompass multiple buildings if they're all on one site and sharing the same upstream IP service, and interconnected via an inter-building LAN.
For a multi-location SME who takes separate internet service for each location from the same ISP, that ISP might allocate a /48 for the SME as a whole, but then allocate a /56 from within that /48 for each physical location.
This aggregation of multiple end sites within one larger subnet allows for simpler firewall policies, VPN settings, etc.