Well...you have to start somewhere. Reference Missions (often, and more familiarly to me, Design Reference Missions) are (hopefully) representative mission profiles which allow the initiation of studies and big picture designs. They are not as formal as requirements although they may serve as the basis for requirements. It is unlikely that any actual mission would exactly follow a Design Reference Mission profile, but they would probably be at least recognizable.
Here's a description from the intro to the Lunar Surface Reference Missions:
It should be noted that the Lunar Surface Reference Mission is a tool,
not a prescription for a program. The selection of tasks to be
accomplished will vary according to the emphases placed on the major
themes of lunar exploration and development and the capabilities of
specific missions. The technology for accomplishing the tasks will
change with time, offering opportunities to improve the concepts
presented here or replace them with other tasks. The Lunar Surface
Reference Mission is intended as a tool for mission planners, to
determine the general level of transportation and surface
infrastructure support that must be provided. It can also be used by
scientists and engineers who have ideas about what should be, or may
be, accomplished on the lunar surface, to examine their ideas in the
context of the resources expected to be available.
I couldn't find a full copy of JSC-07896 "Space Shuttle Baseline Reference Missions" online, but Jim Oberg has an extract posted here. It concerns the very interesting mission where the USAF would launch a shuttle out of Vandenberg on a one-orbit mission to grab a satellite and land.
Mission 3B is defined as a payload retrieval and quick return mission. The total mission duration is one revolution, or approximately 2 hours....The space shuttle, with no payload on board, is launched from WTR on a launch azimuth of 198.6....
Note that this document is from 1973, pretty early in the shuttle design process.