The ones you have mentioned above don't all work the same way and even within each work with special deals as well as regular "travel agent" booking with pre-bought blocks.

Expedia flags its special blocks as Expedia fares (and Travelocity as something similar) wth more restrictions. The ones not marked as such are simply by accessing one of the booking engines. There are a few major booking databases that all subscribe to and similarly use shared booking engines or develop their own.

With the number of changes going on with the fares and availabilty, the booking databases are not always in sync in the real time data and the expedias and travelocities also have smarter algorithms than some others in combining routes and fares.

This explains why there are such discrepencies rather than the differences in business model.