Talking about the difference between a site collection ( SPSite ) and a site ( SPWeb ) , the Site Collection is the unit of authorization for all sites ( SPWebs ) it contains .
I usually see it as a boundary for both security and querying information. In SharePoint we can query information and aggreagate them from different sites ( SPWebs ) but this is limited to the boundaries of a site collection.
In this respect you can think of the query visibility as analogous to aggregating data from two different databases using an SQL Query. In case of Databases, there should be an intermediate step to achieve that and get the correct result set and the same is true for our beloved SharePoint LOL.