My interpretation from reading the 50% AEDG for Small to Medium Office Buildings, along with the relevant section in the document:

Baseline

From GOAL OF THIS GUIDE section:

A building model that complies with ASHRAE Standard 90.1-2004, used as the minimum code-compliant "starting point" for site energy use.

Prototype

From ENERGY MODELING ANALYSIS section:

A building model that can be used to represent a specific building type (typical construction assemblies, internal gains, HVAC systems, etc.). In this document, there are two prototypes: one to represent a small office (20,000 $ft^2$) and one to represent a medium office (50,000 $ft^2$). These prototypes can be used for multiple purposes, and you can read more about a similar set of commercial prototype models maintained by PNNL.

For AEDG, the prototypes were altered to create a baseline version (complies with ASRHAE 90.1-2004) as well as a "improved" version that saves 50% of site energy compared to the baseline version. The changes between these two versions of the prototype models are used to provide AEDG suggestions to apply to your project.

Benchmark

From MULTIDISCIPLINARY RECOMMENDATIONS section:

Also called "business as usual" (BAU), a "starting point" chosen by the design team for energy saving comparisons. This represents the highest allowable site energy use the design team will accept.

Note that the ASHRAE 90.1-2004 "baseline" above was used by the AEDG authors to develop their recommendations, while this "benchmark" is selected by the design team for your project. It could be based on a later ASHRAE 90.1 standard, or any other method, such as:

• U.S. Department of Energy's ENERGY STAR Portfolio Manger
• U.S. Energy Information Administration’s Commercial Buildings Energy Consumption Survey (CBECS)
• California Energy Commission’s California Commercial End-Use Survey (CEUS)