It's called a reference plane because, for both coaxial cable and hollow rectangular waveguides, an ideal connector cuts across the guide in a plane cut.
This is what a waveguide connector looks like, a flange with a plane cut across the guide.
This is a pair of APC-7 (A Precision Connector - 7mm) connectors, designed for precision measurement specifically so that the breaks in the inner and the outer line up to form a plane.
Distances from the 'connector' are measured from this plane.
In a more conventional RF connector like BNC, N-type or SMA, the break in the outer defines the plane.
Any plane across the guide can be taken as a reference plane when doing maths with the phase of RF waves propagating along the guide.
The most usually used planes are those of the connectors, as we are usually interested in reflection coefficients of components with respect to their connectors.
You will however sometimes see evaluation boards for RF components, with a line drawn on the board across a microstrip line, with a note that some S-Parameters are quoted with reference to this plane. This can be useful when you will be copying the reference design, and can choose that cut point as your virtual connector.