A web site is made from a set of "pages" styled by a "theme" connected to a domain name by a "domain". A page has the usual title and text plus it can include "forms", "libraries" and "galleries" are manages as separate entities and can be added to any page and reused multiple times. Each page knows its place in the site hierarchy so a page menu and trail can be added automatically. These six entities are the building blocks for a website.
A company is the container for these entities. Multiple page sets, themes and domains can be managed in one container. The container is called a company whether actually a company or not, maybe "project" could be used to name the container. What is important is that data are shared within a company, eg, pages can be copied or moved from pages set within a company. The data for the websites within one company can be related or completely different however if the data are unrelated it makes sense to split into separate company containers.