That was your first question and a good one! The same paper you went through gave a great example about light on page 20:
http://arxiv.org/PS_cache/hep-ph/pdf/9901/9901399v1.pdf
In the paper we learn light can be described by two different basis, linear verses circular polarization. Linear polarized light can be though of as equal parts left and right circularly polarized light with proper phase difference? In the Faraday Effect the different left and right polarized light propagate at different velocities so the relative phase changes and so rotates the plane of linear polarized light.
The neutrino mass states can be thought of as the circularly polarized light and the flavor states can be thought of as the linear polarized light.
So we have things that can be described in different basis and depending on how these things are produced we chose the proper basis to make life easier?
So thinking of a neutrino think of a three sided tapered cylinder that changes side area with time that that we get to flip in the air, catch, and call its flavor (a tapered cylinder could give three different probables that added up to one and if the cylinder changed shape the probabilities could change)?
I know, cylinders have nothing to do with neutrinos. %^)